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• Proxy / Squid 2.7 / Debian Wheezy 6.7 / lots of TCP Timed-out

  - by Maroon Ibrahim

  i'm facing a lot of TCP timed-out on a busy cache server and here below my sysctl.conf configuration as well as an output of "netstat -st" Kernel 3.2.0-4-amd64 #1 SMP Debian 3.2.57-3 x86_64 GNU/Linux Any advice or help would be highly appreciated #################### Sysctl.conf cat /etc/sysctl.conf net.ipv4.tcp_tw_reuse = 1 net.ipv4.tcp_tw_recycle = 1 fs.file-max = 65536 net.ipv4.tcp_low_latency = 1 net.core.wmem_max = 8388608 net.core.rmem_max = 8388608 net.ipv4.ip_local_port_range = 1024 65000 fs.aio-max-nr = 131072 net.ipv4.tcp_fin_timeout = 10 net.ipv4.tcp_keepalive_time = 60 net.ipv4.tcp_keepalive_intvl = 10 net.ipv4.tcp_keepalive_probes = 3 kernel.threads-max = 131072 kernel.msgmax = 32768 kernel.msgmni = 64 kernel.msgmnb = 65536 kernel.shmmax = 68719476736 kernel.shmall = 4294967296 net.ipv4.ip_forward = 1 net.ipv4.tcp_timestamps = 0 net.ipv4.conf.all.accept_redirects = 0 net.ipv4.tcp_window_scaling = 1 net.ipv4.tcp_sack = 0 net.ipv4.tcp_syncookies = 1 net.ipv4.ip_dynaddr = 1 vm.swappiness = 0 vm.drop_caches = 3 net.ipv4.tcp_moderate_rcvbuf = 1 net.ipv4.tcp_no_metrics_save = 1 net.ipv4.tcp_ecn = 0 net.ipv4.tcp_max_orphans = 131072 net.ipv4.tcp_orphan_retries = 1 net.ipv4.conf.default.rp_filter = 0 net.ipv4.conf.default.accept_source_route = 0 net.ipv4.tcp_max_syn_backlog = 32768 net.core.netdev_max_backlog = 131072 net.ipv4.tcp_mem = 6085248 16227328 67108864 net.ipv4.tcp_wmem = 4096 131072 33554432 net.ipv4.tcp_rmem = 4096 174760 33554432 net.core.rmem_default = 33554432 net.core.rmem_max = 33554432 net.core.wmem_default = 33554432 net.core.wmem_max = 33554432 net.core.somaxconn = 10000 # ################ Netstat results /# netstat -st IcmpMsg: InType0: 2 InType3: 233754 InType8: 56251 InType11: 23192 OutType0: 56251 OutType3: 437 OutType8: 4 Tcp: 20680741 active connections openings 63642431 passive connection openings 1126690 failed connection attempts 2093143 connection resets received 13059 connections established 2649651696 segments received 2195445642 segments send out 183401499 segments retransmited 38299 bad segments received. 14648899 resets sent UdpLite: TcpExt: 507 SYN cookies sent 178 SYN cookies received 1376771 invalid SYN cookies received 1014577 resets received for embryonic SYN_RECV sockets 4530970 packets pruned from receive queue because of socket buffer overrun 7233 packets pruned from receive queue 688 packets dropped from out-of-order queue because of socket buffer overrun 12445 ICMP packets dropped because they were out-of-window 446 ICMP packets dropped because socket was locked 33812202 TCP sockets finished time wait in fast timer 622 TCP sockets finished time wait in slow timer 573656 packets rejects in established connections because of timestamp 133357718 delayed acks sent 23593 delayed acks further delayed because of locked socket Quick ack mode was activated 21288857 times 839 times the listen queue of a socket overflowed 839 SYNs to LISTEN sockets dropped 41 packets directly queued to recvmsg prequeue. 79166 bytes directly in process context from backlog 24 bytes directly received in process context from prequeue 2713742130 packet headers predicted 84 packets header predicted and directly queued to user 1925423249 acknowledgments not containing data payload received 877898013 predicted acknowledgments 16449673 times recovered from packet loss due to fast retransmit 17687820 times recovered from packet loss by selective acknowledgements 5047 bad SACK blocks received Detected reordering 11 times using FACK Detected reordering 1778091 times using SACK Detected reordering 97955 times using reno fast retransmit Detected reordering 280414 times using time stamp 839369 congestion windows fully recovered without slow start 4173098 congestion windows partially recovered using Hoe heuristic 305254 congestion windows recovered without slow start by DSACK 933682 congestion windows recovered without slow start after partial ack 77828 TCP data loss events TCPLostRetransmit: 5066 2618430 timeouts after reno fast retransmit 2927294 timeouts after SACK recovery 3059394 timeouts in loss state 75953830 fast retransmits 11929429 forward retransmits 51963833 retransmits in slow start 19418337 other TCP timeouts 2330398 classic Reno fast retransmits failed 2177787 SACK retransmits failed 742371590 packets collapsed in receive queue due to low socket buffer 13595689 DSACKs sent for old packets 50523 DSACKs sent for out of order packets 4658236 DSACKs received 175441 DSACKs for out of order packets received 880664 connections reset due to unexpected data 346356 connections reset due to early user close 2364841 connections aborted due to timeout TCPSACKDiscard: 1590 TCPDSACKIgnoredOld: 241849 TCPDSACKIgnoredNoUndo: 1636687 TCPSpuriousRTOs: 766073 TCPSackShifted: 74562088 TCPSackMerged: 169015212 TCPSackShiftFallback: 78391303 TCPBacklogDrop: 29 TCPReqQFullDoCookies: 507 TCPChallengeACK: 424921 TCPSYNChallenge: 170388 IpExt: InBcastPkts: 351510 InOctets: -609466797 OutOctets: -1057794685 InBcastOctets: 75631402 #

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• Debugging IO limitation

  - by Martin F

  I have a Fedora box with some severe IO limitations which I have no idea how to debug. The server has a Areca Technology Corp. ARC-1130 12-Port PCI-X to SATA RAID Controller with 12 7200 RPM 1.5 TB disks and a Marvell Technology Group Ltd. 88E8050 PCI-E ASF Gigabit Ethernet Controller. uname -a output: 2.6.32.11-99.fc12.x86_64 #1 SMP Mon Apr 5 19:59:38 UTC 2010 x86_64 x86_64 x86_64 GNU/Linux The server is a file server running Nginx with the stub status module enabled, so I can see the current amount of connections. The problem present itself when I have a high number of simultaneous connections in a writing state. Usually around 350, at this very moment it's at 590 and the server is almost unusable and stuck at 230mbit/s. If I run stop and hit 1 to see CPU core usages I have all 4 cores with around 99% io wait, if I run iotop the nginx workers are the only processes producing any read load, currently at around 25MB/s. I have each of the workers bound to their own core. Initially I figured it was just the disks being bugged. But I've run fscheck and smartmontools checks and found no errors. I also ran an iozone test which you can see the result of here: http://www.pastie.org/951667.txt?key=fimcvljulnuqy2dcdxa Additionally, when the amount of connections are low I have no problem getting a good speed. If I wget over the local network it easily hits 60MB/sec. Right now I just tried putting a file in /dev/shm, then I symlinked a file from the public dir to it and used wget over the local network and only got 50KB/s. Also, if I try to cp /dev/shm/test /root/test it quickly copies around 740MB and then slows down HEAVILY. Again with iotop reporting 99% iowait. I'm not really sure how to go about figuring out what the problems are. It could be a natural disk limitation but then the file from /dev/shm ought to transfer so it seems there's a network limit, but that's fine when there's not many connections. Perhaps it's a TCP stack problem but I really have no idea how to check that. Any suggestions on how to proceed with debugging would be very welcome. If additional information is required then let me know and I'll try to get it. Thanks.

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• Kernel upgrade CentOS 5.3 mount: could not find filesystem '/dev/root'

  - by matt

  We have a CentOS 5.3 x64 server that by default runs kernel version 2.6.18-164.11.1 and we are attempting to upgrade the box to 2.6.31.12 The drive is LVM +ext3, and the problem I'm having is when I upgrade the kernel and attempt to boot from it, no matter what version of the kernel I use, I get /dev/root not found towards the end of the boot process, and the kernel panics, and than reboots. I'm installing the kernel exactly as it says in this doc. I've tried it "The centOS way " using make rpm and than installing that. I've updated my mkinitrd. The most interesting part of this problem is that it has been so frustrating that I decided to try and clean install centos on an identical machine without LVM, and the result is EXACTLY the same. After upgrading the kernel, I get /dev/root not found. Does anyone know how to fix this, or what information would be relevant to remedy it? I'm open to try anything at this point. One more interesting thing about this problem is that in the new version of the kernel, during boot it complains that dm-mapper is started twice, than panics right after that. I've tried this with other kernel versions, and the result is the same. What am I missing here? If you need any more files, please just ask. Linux cg 2.6.18-164.11.1.el5 #1 SMP Wed Jan 20 07:32:21 EST 2010 x86_64 x86_64 x86_64 GNU/Linux /dev/VolGroup00/LogVol00 / ext3 defaults 1 1 LABEL=/boot /boot ext3 defaults 1 2 tmpfs /dev/shm tmpfs defaults 0 0 devpts /dev/pts devpts gid=5,mode=620 0 0 sysfs /sys sysfs defaults 0 0 proc /proc proc defaults 0 0 /dev/VolGroup00/LogVol01 swap swap defaults 0 0 default=1 timeout=5 splashimage=(hd0,0)/grub/splash.xpm.gz hiddenmenu title CentOS (2.6.31.12-rt20) //NOT WORKING!!!! root (hd0,0) kernel /vmlinuz-2.6.31.12-rt20 ro root=/dev/VolGroup00/LogVol00 isolcpus=8,9,10,11,12,13,14,15 panic=10 initrd /initrd-2.6.31.12-rt20.img title CentOS (2.6.18-164.11.1.el5) //WORKING!! root (hd0,0) kernel /vmlinuz-2.6.18-164.11.1.el5 ro root=/dev/VolGroup00/LogVol00 isolcpus=8,9,10,11,12,13,14,15 panic=10 initrd /initrd-2.6.18-164.11.1.el5.img

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• Perl missing while installing nginx on centos

  - by Ahoura Ghotbi

  I am trying to install nginx on my server, however it keeps returning "./configure: error: perl 5.6.1 or higher is required" eventhough I have perl v5.8.8!!!! I have already downloaded perl and trying to configure it using the following command : ./configure --with-http_stub_status_module --with-http_perl_module --with-http_flv_module --add-module=nginx_mod_h264_streaming here is the output : [root@fst nginx-0.8.55]# ./configure --with-http_stub_status_module --with-http_perl_module --with-http_flv_module --add-module=nginx_mod_h264_streaming checking for OS + Linux 2.6.18-308.el5 x86_64 checking for C compiler ... found + using GNU C compiler + gcc version: 4.1.2 20080704 (Red Hat 4.1.2-52) checking for gcc -pipe switch ... found checking for gcc builtin atomic operations ... found checking for C99 variadic macros ... found checking for gcc variadic macros ... found checking for unistd.h ... found checking for inttypes.h ... found checking for limits.h ... found checking for sys/filio.h ... not found checking for sys/param.h ... found checking for sys/mount.h ... found checking for sys/statvfs.h ... found checking for crypt.h ... found checking for Linux specific features checking for epoll ... found checking for sendfile() ... found checking for sendfile64() ... found checking for sys/prctl.h ... found checking for prctl(PR_SET_DUMPABLE) ... found checking for sched_setaffinity() ... found checking for crypt_r() ... found checking for sys/vfs.h ... found checking for nobody group ... found checking for poll() ... found checking for /dev/poll ... not found checking for kqueue ... not found checking for crypt() ... not found checking for crypt() in libcrypt ... found checking for F_READAHEAD ... not found checking for posix_fadvise() ... found checking for O_DIRECT ... found checking for F_NOCACHE ... not found checking for directio() ... not found checking for statfs() ... found checking for statvfs() ... found checking for dlopen() ... not found checking for dlopen() in libdl ... found checking for sched_yield() ... found checking for SO_SETFIB ... not found configuring additional modules adding module in nginx_mod_h264_streaming + ngx_http_h264_streaming_module was configured checking for PCRE library ... found checking for system md library ... not found checking for system md5 library ... not found checking for OpenSSL md5 crypto library ... found checking for zlib library ... found checking for perl + perl version: v5.8.8 built for x86_64-linux-thread-multi ./configure: error: perl 5.6.1 or higher is required

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• HAProxy + Percona XtraDB Cluster

  - by rottmanj

  I am attempting to setup HAproxy in conjunction with Percona XtraDB Cluster on a series of 3 EC2 instances. I have found a few tutorials online dealing with this specific issue, but I am a bit stuck. Both the Percona servers and the HAproxy servers are running ubuntu 12.04. The HAProxy version is 1.4.18, When I start HAProxy I get the following error: Server pxc-back/db01 is DOWN, reason: Socket error, check duration: 2ms. I am not really sure what the issue could be. I have verified the following: EC2 security groups ports are open Poured over my config files looking for issues. I currently do not see any. Ensured that xinetd was installed Ensured that I am using the correct ip address of the mysql server. Any help with this is greatly appreciated. Here are my current config Load Balancer /etc/haproxy/haproxy.cfg global log 127.0.0.1 local0 log 127.0.0.1 local1 notice maxconn 4096 user haproxy group haproxy debug #quiet daemon defaults log global mode http option tcplog option dontlognull retries 3 option redispatch maxconn 2000 contimeout 5000 clitimeout 50000 srvtimeout 50000 frontend pxc-front bind 0.0.0.0:3307 mode tcp default_backend pxc-back frontend stats-front bind 0.0.0.0:22002 mode http default_backend stats-back backend pxc-back mode tcp balance leastconn option httpchk server db01 10.86.154.105:3306 check port 9200 inter 12000 rise 3 fall 3 backend stats-back mode http balance roundrobin stats uri /haproxy/stats MySql Server /etc/xinetd.d/mysqlchk # default: on # description: mysqlchk service mysqlchk { # this is a config for xinetd, place it in /etc/xinetd.d/ disable = no flags = REUSE socket_type = stream port = 9200 wait = no user = nobody server = /usr/bin/clustercheck log_on_failure += USERID #only_from = 0.0.0.0/0 # recommended to put the IPs that need # to connect exclusively (security purposes) per_source = UNLIMITED } MySql Server /etc/services Added the line mysqlchk 9200/tcp # mysqlchk MySql Server /usr/bin/clustercheck # GNU nano 2.2.6 File: /usr/bin/clustercheck #!/bin/bash # # Script to make a proxy (ie HAProxy) capable of monitoring Percona XtraDB Cluster nodes properly # # Author: Olaf van Zandwijk <[email protected]> # Documentation and download: https://github.com/olafz/percona-clustercheck # # Based on the original script from Unai Rodriguez # MYSQL_USERNAME="testuser" MYSQL_PASSWORD="" ERR_FILE="/dev/null" AVAILABLE_WHEN_DONOR=0 # # Perform the query to check the wsrep_local_state # WSREP_STATUS=`mysql --user=${MYSQL_USERNAME} --password=${MYSQL_PASSWORD} -e "SHOW STATUS LIKE 'wsrep_local_state';" 2>${ERR_FILE} | awk '{if (NR!=1){print $2}}' 2>${ERR_FILE}` if [[ "${WSREP_STATUS}" == "4" ]] || [[ "${WSREP_STATUS}" == "2" && ${AVAILABLE_WHEN_DONOR} == 1 ]] then # Percona XtraDB Cluster node local state is 'Synced' => return HTTP 200 /bin/echo -en "HTTP/1.1 200 OK\r\n" /bin/echo -en "Content-Type: text/plain\r\n" /bin/echo -en "\r\n" /bin/echo -en "Percona XtraDB Cluster Node is synced.\r\n" /bin/echo -en "\r\n" else # Percona XtraDB Cluster node local state is not 'Synced' => return HTTP 503 /bin/echo -en "HTTP/1.1 503 Service Unavailable\r\n" /bin/echo -en "Content-Type: text/plain\r\n" /bin/echo -en "\r\n" /bin/echo -en "Percona XtraDB Cluster Node is not synced.\r\n" /bin/echo -en "\r\n" fi

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• 64-bit linux kernel only seeing 3 of 4GB after upgrade...

  - by Blaine

  Hey everyone. I am running Ubuntu 9.04 64-bit on my macbook. I had 2GB of ram before, and everything ran great. I just upgraded to 2x2GB (4GB), but my system only sees 3GB of it. OS X, which I am dual booting, sees all 4GB. Also, my video performance is incredibly lacking. Before the upgrade my compiz benchmark was full at 80fps, and now it is at 22fps with very choppy window dragging. Has anyone ever heard of this on a 64-bit kernel? I just don't quite understand what could be the issue. 10$ uname -a Linux macbook 2.6.28-15-generic #49-Ubuntu SMP Tue Aug 18 19:25:34 UTC 2009 x86_64 GNU/Linux $ free -m total used free shared buffers cached Mem: 2953 1031 1921 0 114 427 -/+ buffers/cache: 489 2463 Swap: 7812 0 7812 9$ lsmod Module Size Used by i915 77960 2 drm 123232 3 i915 binfmt_misc 18572 1 ppdev 16904 0 btusb 21784 2 bridge 63776 0 stp 11140 1 bridge bnep 22912 2 vboxnetadp 109356 0 vboxnetflt 116972 0 vboxdrv 1721612 1 vboxnetflt uvcvideo 69640 0 compat_ioctl32 18304 1 uvcvideo videodev 45184 2 uvcvideo,compat_ioctl32 v4l1_compat 23940 2 uvcvideo,videodev lp 19588 0 parport 49584 2 ppdev,lp snd_hda_intel 557492 3 snd_pcm_oss 52352 0 snd_mixer_oss 24960 1 snd_pcm_oss snd_pcm 99464 2 snd_hda_intel,snd_pcm_oss arc4 10240 2 snd_seq_dummy 11524 0 ecb 11392 2 snd_seq_oss 41984 0 snd_seq_midi 15744 0 snd_rawmidi 33920 1 snd_seq_midi snd_seq_midi_event 16512 2 snd_seq_oss,snd_seq_midi snd_seq 66272 6 snd_seq_dummy,snd_seq_oss,snd_seq_midi,snd_seq_midi_event ath9k 310584 0 snd_timer 34064 2 snd_pcm,snd_seq snd_seq_device 16276 5 snd_seq_dummy,snd_seq_oss,snd_seq_midi,snd_rawmidi,snd_seq mac80211 251528 1 ath9k iTCO_wdt 21712 0 iTCO_vendor_support 12420 1 iTCO_wdt joydev 20992 0 video 29204 0 snd 78920 15 snd_hda_intel,snd_pcm_oss,snd_mixer_oss,snd_pcm,snd_seq_oss,snd_rawmidi,snd_seq,snd_timer,snd_seq_device applesmc 37700 0 output 11648 1 video soundcore 16800 1 snd pcspkr 11136 0 cfg80211 43680 1 mac80211 appletouch 19972 0 isight_firmware 11520 0 input_polldev 12688 1 applesmc intel_agp 39408 1 snd_page_alloc 18704 2 snd_hda_intel,snd_pcm led_class 13064 2 ath9k,applesmc hid_apple 15872 0 usbhid 47040 0 ohci1394 42164 0 ieee1394 108288 1 ohci1394 sky2 63364 0 fbcon 49792 0 tileblit 11264 1 fbcon font 17024 1 fbcon bitblit 14464 1 fbcon softcursor 10368 1 bitblit Some information from dmesg: [ 795.820163] ACPI: EC: GPE storm detected, transactions will use polling mode [ 1762.709516] [drm:i915_getparam] *ERROR* Unknown parameter 6 [ 1763.078130] [drm:i915_getparam] *ERROR* Unknown parameter 6 [ 2362.760889] [drm:i915_getparam] *ERROR* Unknown parameter 6 [ 2416.352084] ACPI: EC: missing confirmations, switch off interrupt mode. [ 3718.721095] [drm:i915_getparam] *ERROR* Unknown parameter 6 [ 3719.108914] [drm:i915_getparam] *ERROR* Unknown parameter 6 [ 4318.773266] [drm:i915_getparam] *ERROR* Unknown parameter 6 [ 9513.813066] CE: hpet increasing min_delta_ns to 15000 nsec [ 9693.815684] npviewer.bin[6736]

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• grep simply fails when used on a few files

  - by Reid

  I've been trying for about the past 30 minutes to get this to work properly. grep is not exactly the most difficult thing to use, so I'm somewhat baffled as to why this won't work. The files I'm trying to use grep on are simple XHTML log files. Their names are in the format [email protected], though I don't think that should matter, and inside is simple XHTML. I copied one such log file to be testfile so you can see the output of some commands and why it's baffling to me: [~/.chatlogs_windows/dec] > whoami reid [~/.chatlogs_windows/dec] > type grep grep is /bin/grep [~/.chatlogs_windows/dec] > uname -a Linux reid-pc 2.6.35-22-generic #33-Ubuntu SMP Sun Sep 19 20:32:27 UTC 2010 x86_64 GNU/Linux [~/.chatlogs_windows/dec] > head -1 /etc/issue Linux Mint 10 Julia [~/.chatlogs_windows/dec] > ls -Alh | grep testfile -rw-r--r-- 1 reid reid 63K 2011-01-10 12:45 testfile [~/.chatlogs_windows/dec] > tail -3 testfile </body> </html> [~/.chatlogs_windows/dec] > file testfile testfile: XML document text [~/.chatlogs_windows/dec] > grep html testfile [~/.chatlogs_windows/dec] > grep body testfile [~/.chatlogs_windows/dec] > grep "</html>" testfile [~/.chatlogs_windows/dec] > grep "</body>" testfile [~/.chatlogs_windows/dec] > cat testfile | grep html [~/.chatlogs_windows/dec] > cat testfile | wc -l 231 [~/.chatlogs_windows/dec] > cat testfile | tail -3 </body> </html> [~/.chatlogs_windows/dec] > chmod a+rw testfile && ls -Alh | grep testfile -rw-rw-rw- 1 reid reid 63K 2011-01-10 12:45 testfile [~/.chatlogs_windows/dec] > grep html testfile That's what I'm attempting to do. I want to just use grep -ri query . in ~/.chatlogs_windows, which normally works perfectly for me... but for some reason, it completely fails at going through these files. If it matters, I copied these files off of my Windows 7 partition. But I chown'd them and gave myself all the appropriate permissions, and other programs (like cat) seem to read them just fine. I also copied testfile to testfile_unix and converted the line endings and tried that, but it didn't work either. I'm using zsh, but I tried it on bash and that failed too. Also, grep works normally: I tried it out on my documents folder and it worked flawlessly. If you need any more information, just let me know. I tried googling around, but I found no reason for grep to simply not work. Thanks in advance.

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• Why does unpartitioned Hitachi HDS5C3020 drive start consuming 50% more power 15 minutes after boot?

  - by Pro Backup

  In a Debian 6.0.6 system there are 74 pieces of 2TB Toshiba DT01ABA200 drives. These drives are identified as Hitachi HDS5C3020BLE630 drives running firmware revision MZ4OAAB0. 64 Drives attached via HP SAS expander cards to an LSI 2008 SAS controller, another 5 drives are connected directly to the mainboard, 4 drives are connected to a Sil based PCI controller and last 1 drive is only powered and has no data cable connected. The controller LSI and Sil card's their onboard BIOS are both disabled and the mpt2sas and sata_sil modules are removed from the Linux debian 2.6.32-5-amd64 #1 SMP Sun Sep 23 10:07:46 UTC 2012 x86_64 GNU/Linux kernel. The mpt2sas module is loaded after boot using a modprobe command in /etc/rc.local. These 74 drives are not partitioned, neither formatted and also not mounted. The system consumes: with 0 drives: 70.6 - 70.9 Watt (also 15 minutes after boot); with 74 drives: 330 - 360 Watt, just after boot (is equivalent to 3.5 - 3.9W per drive in idle state); with 74 drives: 420 - 466 Watt, each time in the 15th minute of uptime (is equivalent to 4.7 - 5.3W per drive in idle state). The drive specification lists 4.7W as read/write, and 3.3W as idle power consumption. The increased power consumption is most likely on the 5V line, because after roughly 1 minute an "over current protection" (OCP) of the power supply (PSU) shuts down the power. The used PSU is a single rail model with an OCP of 122A on the 12V line and 55A on the 5V line. Regression: It doesn't matter whether the drive its APM value is set to disabled or 1 (maximum power saving). The operating system records no read/write activity in /proc/diskstats. The values there are identical (28 read, 0 write operations) as immediately after the modprobe operation. Can't test what happens when booting into the mainboard it's BIOS - to exclude any OS intervention - because the Super Micro X8SI6-F mainboard running firmware 06/27/12 has a bug that incorrectly reads a +74.0 C CPU sensor temperature as "High" in BIOS mode, and shuts down the power after 1 minute. What might be causing the drive read/write activity on all drives in the 15th minute after boot and how to prevent it from happening?

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• Hybrid gmail MX + postfix for local accounts

  - by krunk

  Here's the setup: We have a domain, mydomain.com. Everything is on our own server, except general email accounts which are through gmail. Currently gmail is set as the MX record. The server also has various email aliases it needs to support for bug trackers and such. e.g. [email protected] |/path/to/issuetracker.script I'm struggling with a setup that allows the following, both locally and from user's email clients. guser1 - has a gmail account and a local account guser2 - only has a gmail account bugs - has a pipe alias in /etc/aliases for issue tracker Scenarios mail to [email protected] from local host (crons and such) needs to go to gmail account mail to [email protected] from local host mail to [email protected] needs to be piped to the local issue tracker script So, the first stab was creating a transport map. In this scenario, the our server would be set as teh MX and guser* destined emails are sent to gmail. Put the gmail users in a map like so: [email protected] smtp:gmailsmtp:25 [email protected] smtp:gmailsmtp:25 Problems: Ignores extensions such as [email protected] Only works if append_at_myorigin = no (if set to yes, gmail refuses to connect with: E4C7E3E09BA3: to=, relay=none, delay=0.05, delays=0.02/0.01/0.02/0, dsn=4.4.1, status=deferred (connect to gmail-smtp-in.l.google.com[209.85.222.57]:25: Connection refused)) since append_at_myorigin is set to no, all received emails have (unknown sender) The second stab was to set explicit localhost aliases in /etc/aliases and do a domain wide forward on mydomain. This too requires setting the local server as the MX: root: root@localhost # transport mydomain.com smtp:gmailsmtp:25 Problems: * If I create a transport map for a domain that matches "$myhostname", the aliases file is never parsed. So when a local user (or daemon) sends an email like: mail -s "testing" root < text.txt Postfix ignores the /etc/alias entry and maps to [email protected] and attempts to send it to the gmail transport mapping. Third stab: Create a subdomain for the bugs, something like bugs.mydomain.com. Set the MX for this domain to local server and leave the MX for mydomain.com to the Gmail server. Problems: * Does not solve the issue with local accounts. So when the bug tracker responds to an email from [email protected], it uses a local transport and the user never receives the email. % postconf -n alias_database = hash:/etc/aliases alias_maps = hash:/etc/aliases append_at_myorigin = no append_dot_mydomain = no biff = no config_directory = /etc/postfix inet_interfaces = all mailbox_command = procmail -a "$EXTENSION" mailbox_size_limit = 0 mydestination = $myhostname, localhost.$myhostname, localhost myhostname = mydomain.com mynetworks = 127.0.0.0/8 [::ffff:127.0.0.0]/104 [::1]/128 myorigin = /etc/mailname readme_directory = no recipient_delimiter = + relayhost = smtp_tls_cert_file = /etc/ssl/certs/kspace.pem smtp_tls_enforce_peername = no smtp_tls_key_file = /etc/ssl/certs/kspace.pem smtp_tls_note_starttls_offer = yes smtp_tls_scert_verifydepth = 5 smtp_tls_session_cache_database = btree:${data_directory}/smtp_scache smtp_use_tls = yes smtpd_banner = $myhostname ESMTP $mail_name (Debian/GNU) smtpd_recipient_restrictions = permit_mynetworks, reject_invalid_hostname, reject_non_fqdn_sender, reject_non_fqdn_recipient, reject_unknown_sender_domain, reject_unknown_recipient_domain, reject_unauth_destination smtpd_tls_ask_ccert = yes smtpd_tls_req_ccert = no smtpd_tls_session_cache_database = btree:${data_directory}/smtpd_scache tls_random_source = dev:/dev/urandom transport_maps = hash:/etc/postfix/transport

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• Reasons for missing IP info in `last` output on pts logins?

  - by Mike Pennington

  I have five CentOS 6 linux systems at work, and encountered a rather strange issue that only seems to happen with my userid across all the linux systems I have... This is an example of the problem from entries I excepted from the last command... mpenning pts/19 Fri Nov 16 10:32 - 10:35 (00:03) mpenning pts/17 Fri Nov 16 10:21 - 10:42 (00:21) bill pts/15 sol-bill.local Fri Nov 16 10:19 - 10:36 (00:16) mpenning pts/1 192.0.2.91 Fri Nov 16 10:17 - 10:49 (12+00:31) kkim14 pts/14 192.0.2.225 Thu Nov 15 18:02 - 15:17 (4+21:15) gduarte pts/10 192.0.2.135 Thu Nov 15 12:33 - 08:10 (11+19:36) gduarte pts/9 192.0.2.135 Thu Nov 15 12:31 - 08:10 (11+19:38) kkim14 pts/0 :0.0 Thu Nov 15 12:27 - 15:17 (5+02:49) gduarte pts/6 192.0.2.135 Thu Nov 15 11:44 - 08:10 (11+20:25) kkim14 pts/13 192.0.2.225 Thu Nov 15 09:56 - 15:17 (5+05:20) kkim14 pts/12 192.0.2.225 Thu Nov 15 08:28 - 15:17 (5+06:49) kkim14 pts/11 192.0.2.225 Thu Nov 15 08:26 - 15:17 (5+06:50) dspencer pts/8 192.0.2.130 Wed Nov 14 18:24 still logged in mpenning pts/18 alpha-console-1. Mon Nov 12 14:41 - 14:46 (00:04) You can see two of my pts login entries above that do not have a source IP address associated with them. My CentOS machines have as many as six other users that share the systems, but the mpenning userid is the only one that has this issue. Approximately 5% of my logins see this issue, but no other usernames exhibit this behavior. Questions Given the kind of scripts I keep on these systems (which control much of our network infrastructure), I'm a little spooked by this and would like to understand what would cause my logins to occasionally miss source addresses. Is there anything (other than malicious activity) that would reasonably explain the behavior? Other than bash history timestamping, are there other things I can do to track the issue down? Informational Since this started happening, I enabled bash history time-stamping (i.e. HISTTIMEFORMAT="%y-%m-%d %T " in .bash_profile) and also added a few other bash history hacks; however, that does not give clues to what happened during the previous occurrences. All the systems run CentOS 6.3... [mpenning@typo ~]$ uname -a Linux typo.local 2.6.32-279.9.1.el6.x86_64 #1 SMP Tue Sep 25 21:43:11 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux [mpenning@typo ~]$ EDIT If I use last -i mpenning, I see entries like this... mpenning pts/19 0.0.0.0 Fri Nov 16 10:32 - 10:35 (00:03) mpenning pts/17 0.0.0.0 Fri Nov 16 10:21 - 10:42 (00:21)

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• 2xAMD Opteron 6128 with libvirt, Physical CPU 13 doesn't exist

  - by yak

  I need help with libvirt(?) problem. Server specs: ProLiant DL165 G7 2x AMD Opteron(tm) Processor 6128 System: Debian GNU/Linux testing (wheezy) 3.2.0-3-amd64 libvirt 0.9.12-5 kvm 1:1.1.2+dfsg-2 $ grep processor /proc/cpuinfo | wc -l 16 $ virsh nodeinfo setlocale: No such file or directory CPU model: x86_64 CPU(s): 16 CPU frequency: 800 MHz CPU socket(s): 2 Core(s) per socket: 4 Thread(s) per core: 1 NUMA cell(s): 1 Memory size: 66114200 KiB $ virsh capabilities .. <topology> <cells num='4'> <cell id='0'> <cpus num='4'> <cpu id='0'/> <cpu id='1'/> <cpu id='2'/> <cpu id='3'/> </cpus> </cell> <cell id='1'> <cpus num='4'> <cpu id='4'/> <cpu id='5'/> <cpu id='6'/> <cpu id='7'/> </cpus> </cell> <cell id='2'> <cpus num='4'> <cpu id='12'/> <cpu id='13'/> <cpu id='14'/> <cpu id='15'/> </cpus> </cell> <cell id='3'> <cpus num='4'> <cpu id='8'/> <cpu id='9'/> <cpu id='10'/> <cpu id='11'/> </cpus> </cell> </cells> </topology> .. $ virsh vcpupin vm 0 13,12,11,10,9,8,7,6,5 error: Physical CPU 13 doesn't exist. error: cpulist: Invalid format. Question? Why my VM Guests use only first 8 CPUs and next 8 are idling? $ for host in virsh list | awk '{print $2}'; do virsh vcpuinfo $host; done | grep ^CPU: | sort | uniq CPU: 0 CPU: 1 CPU: 2 CPU: 3 CPU: 4 CPU: 5 CPU: 6 CPU: 7 Any ideas how to change it?

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• PHP Sessions suddenly not working

  - by styrken

  Out of no where my php sessions does not work anymore. The server have been running fine for several months. I'am running Ubuntu 11.10 (GNU/Linux 3.0.0-14-server x86_64) with nginx/1.0.11 and php 5.3.19-1~dotdeb.0 Session info copied from phpinfo() Session Support enabled Registered save handlers files user memcached Registered serializer handlers php php_binary wddx Directive Local Value Master Value session.auto_start Off Off session.bug_compat_42 Off Off session.bug_compat_warn Off Off session.cache_expire 180 180 session.cache_limiter nocache nocache session.cookie_domain no value no value session.cookie_httponly Off Off session.cookie_lifetime 0 0 session.cookie_path / / session.cookie_secure Off Off session.entropy_file no value no value session.entropy_length 0 0 session.gc_divisor 1000 1000 session.gc_maxlifetime 1440 1440 session.gc_probability 0 0 session.hash_bits_per_character 5 5 session.hash_function 0 0 session.name PHPSESSID PHPSESSID session.referer_check no value no value session.save_handler files files session.save_path /tmp /tmp session.serialize_handler php php session.use_cookies On On session.use_only_cookies On On session.use_trans_sid 0 0 I have setup the following php script to test with: error_reporting(E_ALL); ini_set('display_errors', true); error_log($_SERVER['REMOTE_ADDR'] . ' visited test page'); if(session_start()) echo "Session started <br />"; else echo "Session failed <br />"; echo '<a href="?', time(), '">refresh</a>', "\n"; echo '<pre>'; echo 'session id: ', session_id(), "\n"; $sessionfile = ini_get('session.save_path') . '/' . 'sess_'.session_id(); echo 'session file: ', $sessionfile, ' '; if ( file_exists($sessionfile) ) { echo 'size: ', filesize($sessionfile), "\n"; echo '# ', file_get_contents($sessionfile), ' #'; } else { echo ' does not exist'; } echo PHP_EOL; $_SESSION['number'] = (int) @$_SESSION['number'] + 1; var_dump($_SESSION); echo "</pre>\n"; session_write_close(); echo 'done.'; It tells me that the session file exists, but my session id changes on each refresh.. What is going wrong? There is no output to any error logs at all.. :/ Please help!

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• Sarg report error

  - by amyassin

  I have a proxy server that runs Ubuntu Server 11.10, Squid 2.7.STABLE9. I installed sarg (version 2.3.1 Sep-18-2010) to generate reports using the ordinary apt-get install, and added a cron job to generate a report of the day every 5 minutes (that will overwrite the 5-minutes-older one): */5 * * * * /root/proxy_report.sh And the content of /root/proxy_report.sh is: #!/bin/bash /usr/bin/sarg -nd `date +"%d/%m/%Y"` > /dev/null 2>&1 And I added another cron job to generate a full report every hour at :32 (not to collide with the 5 minutes job): */32 * * * * /root/proxy_report_full.sh And the content of /root/proxy_report_full.sh is : #!/bin/bash /usr/bin/sarg -n > /dev/null 2>&1 And I added a small script to remove the yesterday full report (the full report that ends in yesterday that won't be overwritten by the new today full report) in /etc/rc.local to run at startup: /usr/bin/rm_yesterday.sh &>> /var/log/rm_yesterday Where /usr/bin/rm_yesterday.sh: #!/bin/bash find /var/www/sarg/ | grep `date -d Apr1 +"%Y%b%d"`-* | grep -v `date +"%Y%b%d"` | xargs rm -rf * Apr1 is the starting date of the proxy... ** I've placed it in /usr/bin to be mounted early at startup... That arrangement went OK for about a month and a half, except for one time I noticed some errors and reports wasn't generated, and fixed that by making an offset (the two minutes in 32 of the second cron job). However, it then started not to generate reports anymore. By manually trying to generate it it gives the following error: root@proxy-server:~# sarg -n SARG: getword_atoll loop detected after 3 bytes. SARG: Line="154 192.168.10.40 TCP_MISS/200 39 CONNECT www.google.com" SARG: Record="154 192.168.10.40 TCP_MISS/200 39 CONNECT www.google.com" SARG: searching for 'x2f' SARG: getword backtrace: SARG: 1:sarg() [0x8050a4a] SARG: 2:sarg() [0x8050c8b] SARG: 3:sarg() [0x804fc2e] SARG: 4:/lib/i386-linux-gnu/libc.so.6(__libc_start_main+0xf3) [0x129113] SARG: 5:sarg() [0x80501c9] SARG: Maybe you have a broken date in your /var/log/squid/access.log file When I looked to /var/log/squid/ folder, I noticed that it contains some rotated logs: root@proxy-server:~# ls /var/log/squid/ access.log access.log.1 cache.log cache.log.1 store.log store.log.1 So maybe sarg installed logrotate with it? Or it comes with the standard Ubuntu? I don't remember I installed it manuallly. The question is: What could've gone wrong? Does it have something to do with rotating the log? How can I trace the error and start generating reports again?

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• Thinkpad speaker turns mute - Linux Codec issue?

  - by Curlew

  At some point a few days ago the speakers on my Lenovo Thinkpad T410 (Model number: 2537A11) suddenly stopped working randomly. This error happens every time I watch a video or listen to a music file. The sound just abruptly stops. At the moment, I can't produce a single sound no matter what I do. I am using Debian GNU/Linux on this laptop and there doesn't appear to be anything else wrong (the fan is working, no abnormal heat (staying around ~40°C), no other obvious errors or problems). Here is the output of a nice program someone pointed me to: martin@martin:~/Downloads$ sudo python run.py --monitor Using temporary directory: /dev/shm/hda-analyzer You may remove this directory when finished or if you like to download the most recent copy of hda-analyzer tool. Downloading file hda_analyzer.py Downloading file hda_guilib.py Downloading file hda_codec.py Downloading file hda_proc.py Downloading file hda_graph.py Downloading file hda_mixer.py Downloaded all files, executing hda_analyzer.py Watching 1 cards ====================================== Sound is working normally and then it stops and the following lines appear: Diff for codec 0/0 (0x14f15069): --- +++ @@ -164,17 +164,17 @@ Power: setting=D0, actual=D0 Node 0x1f [Pin Complex] wcaps 0x400501: Stereo Pincap 0x00000010: OUT Pin Default 0x901701f0: [Fixed] Speaker at Int N/A Conn = Analog, Color = Unknown DefAssociation = 0xf, Sequence = 0x0 Misc = NO_PRESENCE Pin-ctls: 0x40: OUT - Power: setting=D0, actual=D0 + Power: setting=D3, actual=D3 Connection: 2 0x10* 0x11 Node 0x20 [Pin Complex] wcaps 0x400781: Stereo Digital Pincap 0x00000010: OUT Pin Default 0x40f001f0: [N/A] Other at Ext N/A Conn = Unknown, Color = Unknown DefAssociation = 0xf, Sequence = 0x0 Misc = NO_PRESENCE And now there is also an error in the dmesg output hda-intel: IRQ timing workaround is activated for card #0. Suggest a bigger bdl_pos_adj. I changed the bdl_pos_adj to various numbers (-1, 0, 64, 1024) and either there is no change at all or dmesg reports that the adjustment is too big. I wonder if this bdl_pos_adj is the real reason for the error. Here is my hardware information provided by alsa-info.sh website. Okay, i did some serious testing and even installed Windows and now i officially conclude that this is a hard-ware related issue with my Laptop speakers. Reason: The error occurs in my installed Debian Linux, an Ubuntu Live distribution and Windows XP No error-message appears in all of the OS. The sound just keeps running and i can't hear a thing. I tested different setups, including OSS, ALSA and the pulseaudio server on top If i use my new usb-headphones i can hear sound all the time without any sudden silences. So obviously, although hard to believe, my laptop speakers are not okay (never heard of similar cases). I'll award the bounty to anyone who can point me to good tutorials or the procedure how to exchange my T410 speakers (i still have warranty. The laptop was bought in Germany, but now i am in Denmark). Or to someone who can explain me the output from hda-analyzer (big log above).

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• Can't validate mine, sudo nor root in Debian "Jessie" Gnome anymore?

  - by Janar

  I'm Debian beginner & GUI guy in a bit of trouble? Can't login as sudo/gksu/root/su nor as (main/super)user after removed user password via Gnome-user-settings. History of actions (Probably irrelevant though) Installed Debian "Jessie" GNU/Linux with xFce GUI (en-US) as only OS. HardWare is ThinkPad w510. Skipped root user password in setup, to get sudo for superuser easily. Logged in (as always had) with Gnome (3.4.x), not once with xFCE. (installed Xfce. Installed xFce only to achieve more control (easier management) over packages this way, to set-up gnome much more by mine likes. Added more jessie repros (same ones as in Wheesy stable by default but for Jessie as, Jessie only had repros for security updates by default). Installed lots of gtk(3) & gnome(3) based soft; (- restarted again after this) Installed propietary graphics card driver for mine nvidia quadro. (- restarted once again after that one) Installed more stuff related to mine work/school/devel. The actual problem Had a plan to restart again, but wanted to set up auto-login first, instead set user password to none (don't ask why / perhaps caused by being awake for a looooong time), noticed it, and set also to auto-login, but couldn't undo mine previous mistake to create new password for me. As mine password is set to none I would have expected that simply return in pass prompt for emty password field would do, but it won't authenticate. I tried Alt+F2 "gksu gedit" as well as: sudo wget "https://www.some-page.eu/file.ext" and "su" in terminals, none has applied (quite logical actually - as I'm sudoer and highest ranked super user, besides only user in computer). Current stand Everything worked & still works nice after this accident, besides this password prompts part. To spoked to log-out nor restart. Synaptic package-manager is still open with root rights (only one, that has left open prior to the issue and not closed since, just in case). Goggled for help and read some manuals/faqs/how-tos - mostly lead to sudoers file management, but not found one specifically for mine issue - so still not any smarter. Really hope, that I don't have to redo OS inst all over again, by just one stupid mistake. Thanks for your reply :-)

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• Why is domU faster than dom0 on IO?

  - by Paco

  I have installed debian 7 on a physical machine. This is the configuration of the machine: 3 hard drives using RAID 5 Strip element size: 1M Read policy: Adaptive read ahead Write policy: Write Through /boot 200 MB ext2 / 15 GB ext3 SWAP 10GB LVM rest (~500GB) emphasized text I installed postgresql, created a big database (over 1GB). I have an SQL request that takes a lot of time to run (a SELECT statement, so it only reads data from the database). This request takes approximately 5.5 seconds to run. Then, I installed XEN, created a domU, with another debian distro. On this OS, I also installed postgresql, with the same database. The same SQL request takes only 2.5 seconds to run. I checked the kernel on both dom0 and domU. uname-a returns "Linux debian 3.2.0-4-amd64 #1 SMP Debian 3.2.41-2+deb7u2 x86_64 GNU/Linux" on both systems. I checked the kernel parameters, which are approximately the same. For those that are relevant, I changed their values to make them match on both systems using sysctl. I saw no changes (the requests still take the same amount of time). After this, I checked the file systems. I used ext3 on domU. Still no changes. I installed hdparm, and ran hdparm -Tt on both systems, on all my partitions on both systems, and I get similar results. Now, I am stuck, I don't know what is different, and what could be the cause of such a big difference. Additional Info: Debian runs on a Dell server PowerEdge 2950 postgresql: 9.1.9 (both dom0 and domU) xen-linux-system: 3.2.0 xen-hypervisor: 4.1 Thanks EDIT: As Krzysztof Ksiezyk suggested, it might be due to some file caching system. I ran the dd command to test both the read and write speed. Here is domU: root@test1:~# dd if=/dev/zero of=/root/dd count=5MB bs=1MB ^C2020+0 records in 2020+0 records out 2020000000 bytes (2.0 GB) copied, 18.8289 s, 107 MB/s root@test1:~# dd if=/root/dd of=/dev/null count=5MB bs=1MB 2020+0 records in 2020+0 records out 2020000000 bytes (2.0 GB) copied, 15.0549 s, 134 MB/s And here is dom0: root@debian:~# dd if=/dev/zero of=/root/dd count=5MB bs=1MB ^C1693+0 records in 1693+0 records out 1693000000 bytes (1.7 GB) copied, 8.87281 s, 191 MB/s root@debian:~# dd if=/root/dd of=/dev/null count=5MB bs=1MB 1693+0 records in 1693+0 records out 1693000000 bytes (1.7 GB) copied, 0.501509 s, 3.4 GB/s What can be the cause of this caching system? And how can we "fix" it? Can we apply it to dom0? EDIT 2: I switched my virtual disk type. To do so I followed this article. I did a dd if=/dev/vg0/test1-disk of=/mnt/test1-disk.img bs=16M Then in /etc/xen/test1.cfg, I changed the disk parameter to use file: instead of phy: it should have removed the file caching, but I still get the same numbers (domU being much faster for Postgres)

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• tc rules block traffic from some hosts at network

  - by user139430

  I have a problem I can not solve. The script, which sets the rules for traffic shaping is blocking the traffic from some hosts.If I remove all the rules, then it works. I can not understand why? Here is my script... #!/bin/sh cmdTC=/sbin/tc rateLANDl="60mbit" ceilLANDl="60mbit" rateLANUl="40mbit" ceilLANUl="40mbit" quantLAN="1514" # Nowaday bandwidth limit set to 100mbit. # We devide it with 60mbit download and 40mbit upload bandthes. rateHiDl="30mbit" ceilHiDl="60mbit" rateHiUl="20mbit" ceilHiUl="40mbit" quantHi="1514" rateLoDl="30mbit" ceilLoDl="60mbit" rateLoUl="20mbit" ceilLoUl="40mbit" quantLo="1514" devNIF=eth0 devFIF=ifb0 modprobe ifb ip link set $devFIF up 2>/dev/null #exit 0 ################################################################################################ # Remove discuiplines from network and fake interfaces ################################################################################################ $cmdTC qdisc del dev $devNIF root 2>/dev/null $cmdTC qdisc del dev $devFIF root 2>/dev/null $cmdTC qdisc del dev $devNIF ingress 2>/dev/null if [ "$1" = "down" ]; then exit 0 fi ################################################################################################ # Create discuiplines for network interface ################################################################################################ $cmdTC qdisc add dev $devNIF root handle 1:0 htb default 12 # Create classes for network interface $cmdTC class add dev $devNIF parent 1:0 classid 1:1 htb rate ${rateLANDl} ceil ${ceilLANDl} quantum ${quantLAN} $cmdTC class add dev $devNIF parent 1:1 classid 1:11 htb rate ${rateHiDl} ceil ${ceilHiDl} quantum ${quantHi} $cmdTC class add dev $devNIF parent 1:1 classid 1:12 htb rate ${rateLoDl} ceil ${ceilLoDl} quantum ${quantLo} $cmdTC qdisc add dev $devNIF parent 1:11 handle 111: sfq perturb 10 $cmdTC qdisc add dev $devNIF parent 1:12 handle 112: sfq perturb 10 # Create filters for network interface $cmdTC filter add dev $devNIF protocol all parent 1:0 u32 match ip dst 10.252.2.0/24 flowid 1:11 $cmdTC filter add dev $devNIF protocol all parent 111: handle 111 flow hash keys dst divisor 1024 baseclass 1:11 $cmdTC filter add dev $devNIF protocol all parent 112: handle 112 flow hash keys dst divisor 1024 baseclass 1:12 ################################################################################################ # Create discuiplines for fake interface ################################################################################################ $cmdTC qdisc add dev $devFIF root handle 1:0 htb default 12 # Create classes for network interface $cmdTC class add dev $devFIF parent 1:0 classid 1:1 htb rate ${rateLANUl} ceil ${ceilLANUl} quantum ${quantLAN} $cmdTC class add dev $devFIF parent 1:1 classid 1:11 htb rate ${rateHiUl} ceil ${ceilHiUl} quantum ${quantHi} $cmdTC class add dev $devFIF parent 1:1 classid 1:12 htb rate ${rateLoUl} ceil ${ceilLoUl} quantum ${quantLo} $cmdTC qdisc add dev $devFIF parent 1:11 handle 111: sfq perturb 10 $cmdTC qdisc add dev $devFIF parent 1:12 handle 112: sfq perturb 10 # Create filters for network interface $cmdTC filter add dev $devFIF protocol all parent 1:0 u32 match ip src 10.252.2.0/24 flowid 1:11 $cmdTC filter add dev $devFIF protocol all parent 111: handle 111 flow hash keys src divisor 1024 baseclass 1:11 $cmdTC filter add dev $devFIF protocol all parent 112: handle 112 flow hash keys src divisor 1024 baseclass 1:12 ################################################################################################ # Create redirect discuiplines from network to fake interface ################################################################################################ $cmdTC qdisc add dev $devNIF handle ffff:0 ingress $cmdTC filter add dev $devNIF parent ffff:0 protocol all u32 match u32 0 0 action mirred egress redirect dev $devFIF Here is my /etc/modules: loop ifb ppp_mppe nf_conntrack_pptp nt_conntrack_proto_gre nf_nat_pptp nf_nat_proto_gre The system is Linux wall 2.6.32-5-amd64 #1 SMP Sun Sep 23 10:07:46 UTC 2012 x86_64 GNU/Linux

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• Linux clock loses 10 minutes every week

  - by PaKempf

  One of my linux server's clock loses 10 minutes every now and then, nearly every week. I update the time so it stays correct, and although it doesn't really bother me, i'd like to fix it. I've been searching around a bit. Nothing can be responsible in the crontab, and i can't find any related message in the logs. Some people seem to use ntp to fix that kind of issue, but i'd prefer not to use an unecessary component on it. Uname result : Linux unis-monitor 2.6.32-5-686 #1 SMP Mon Feb 25 01:04:36 UTC 2013 i686 GNU/Linux Cat message : cat messages Jul 14 06:25:06 unis-monitor rsyslogd: [origin software="rsyslogd" swVersion="4.6.4" x-pid="882" x-info="http://www.rsyslog.com"] rsyslogd was HUPed, type 'lightweight'. Jul 15 06:25:05 unis-monitor rsyslogd: [origin software="rsyslogd" swVersion="4.6.4" x-pid="882" x-info="http://www.rsyslog.com"] rsyslogd was HUPed, type 'lightweight'. Cat syslog cat syslog Jul 15 06:25:05 unis-monitor rsyslogd: [origin software="rsyslogd" swVersion="4.6.4" x-pid="882" x-info="http://www.rsyslog.com"] rsyslogd was HUPed, type 'lightweight'. Jul 15 06:39:01 unis-monitor /USR/SBIN/CRON[15272]: (root) CMD ( [ -x /usr/lib/php5/maxlifetime ] && [ -d /var/lib/php5 ] && find /var/lib/php5/ -type f -cmin +$(/usr/lib/php5/maxlifetime) -delete) Jul 15 07:09:01 unis-monitor /USR/SBIN/CRON[15465]: (root) CMD ( [ -x /usr/lib/php5/maxlifetime ] && [ -d /var/lib/php5 ] && find /var/lib/php5/ -type f -cmin +$(/usr/lib/php5/maxlifetime) -delete) Jul 15 07:17:01 unis-monitor /USR/SBIN/CRON[15521]: (root) CMD ( cd / && run-parts --report /etc/cron.hourly) Jul 15 07:39:01 unis-monitor /USR/SBIN/CRON[15662]: (root) CMD ( [ -x /usr/lib/php5/maxlifetime ] && [ -d /var/lib/php5 ] && find /var/lib/php5/ -type f -cmin +$(/usr/lib/php5/maxlifetime) -delete) Jul 15 08:09:01 unis-monitor /USR/SBIN/CRON[15855]: (root) CMD ( [ -x /usr/lib/php5/maxlifetime ] && [ -d /var/lib/php5 ] && find /var/lib/php5/ -type f -cmin +$(/usr/lib/php5/maxlifetime) -delete) Jul 15 08:17:01 unis-monitor /USR/SBIN/CRON[15911]: (root) CMD ( cd / && run-parts --report /etc/cron.hourly) Jul 15 08:39:01 unis-monitor /USR/SBIN/CRON[16052]: (root) CMD ( [ -x /usr/lib/php5/maxlifetime ] && [ -d /var/lib/php5 ] && find /var/lib/php5/ -type f -cmin +$(/usr/lib/php5/maxlifetime) -delete) Jul 15 09:09:01 unis-monitor /USR/SBIN/CRON[16273]: (root) CMD ( [ -x /usr/lib/php5/maxlifetime ] && [ -d /var/lib/php5 ] && find /var/lib/php5/ -type f -cmin +$(/usr/lib/php5/maxlifetime) -delete) So if you have any clue of where to look or what i could use to monitor those date change ? Here is some more infos : the server is a virtual server hosted on HyperV on a win 2012 server. Don't know if it changes anything, seen the other servers hosted don't have this issue...

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• Why is Linux choosing the wrong source ip address

  - by Scheintod

  and what to do to let it choose the right one? This all happens inside an OpenVZ container: The Host is Debian/Wheezy with Redhat/OpenVZ Kernel: root@mycl2:~# uname -a Linux mycl2 2.6.32-openvz-042stab081.5-amd64 #1 SMP Mon Sep 30 16:40:27 MSK 2013 x86_64 GNU/Linux The container has two (virtual) network interfaces. One in public and one in private address-space: root@mycl2:~# ifconfig lo Link encap:Local Loopback inet addr:127.0.0.1 Mask:255.0.0.0 inet6 addr: ::1/128 Scope:Host UP LOOPBACK RUNNING MTU:16436 Metric:1 RX packets:0 errors:0 dropped:0 overruns:0 frame:0 TX packets:0 errors:0 dropped:0 overruns:0 carrier:0 collisions:0 txqueuelen:0 RX bytes:0 (0.0 B) TX bytes:0 (0.0 B) venet0 Link encap:UNSPEC HWaddr 00-00-00-00-00-00-00-00-00-00-00-00-00-00-00-00 inet addr:127.0.0.2 P-t-P:127.0.0.2 Bcast:0.0.0.0 Mask:255.255.255.255 UP BROADCAST POINTOPOINT RUNNING NOARP MTU:1500 Metric:1 RX packets:475 errors:0 dropped:0 overruns:0 frame:0 TX packets:775 errors:0 dropped:0 overruns:0 carrier:0 collisions:0 txqueuelen:0 RX bytes:32059 (31.3 KiB) TX bytes:56309 (54.9 KiB) venet0:0 Link encap:UNSPEC HWaddr 00-00-00-00-00-00-00-00-00-00-00-00-00-00-00-00 inet addr:80.123.123.29 P-t-P:80.123.123.29 Bcast:80.123.123.29 Mask:255.255.255.255 UP BROADCAST POINTOPOINT RUNNING NOARP MTU:1500 Metric:1 venet0:1 Link encap:UNSPEC HWaddr 00-00-00-00-00-00-00-00-00-00-00-00-00-00-00-00 inet addr:10.0.1.29 P-t-P:10.0.1.29 Bcast:10.0.1.29 Mask:255.255.255.255 UP BROADCAST POINTOPOINT RUNNING NOARP MTU:1500 Metric:1 The route to the private network is set manually: root@mycl2:~# route -n Kernel IP routing table Destination Gateway Genmask Flags Metric Ref Use Iface 10.0.0.0 0.0.0.0 255.0.0.0 U 0 0 0 venet0 0.0.0.0 0.0.0.0 0.0.0.0 U 0 0 0 venet0 Tring to ping others on the private network leads to the wrong source address been choosen: root@mycl2:~# ip route get 10.0.1.26 10.0.1.26 dev venet0 src 80.123.123.29 cache mtu 1500 advmss 1460 hoplimit 64 Why is this and what can I do about it? EDIT: If I create the route with (thanks to Joshua) ip route add 10.0.0.0/8 dev venet0 src 10.0.1.29 it is working. But according to man ip-route the src parameter should only set the source-ip if this route is chosen. But if this route is chosen then the source-ip would be that anyway.

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• What server setup for a small web development company? [closed]

  - by Giordano

  I co-own a company with a friend of mine and we have decided to buy a new server to support our business (our current server is an Asus EEE Box, working great but too limited :) ). I should mention that we are web developers but occasionally we do small-office sys admin. Thus, 99% of time we work on GNU/Linux (mainly Ubuntu) but from time to time we need to setup a Windows environment to assist some customers (e.g. setup a temporary SQL Server 2008). Our requirements: Low budget: we don't want the cheapest solution out there but we can't afford to spend too much. Budget could be ~1000-1500€ (before VAT) Robustness: we would like to setup a RAID array and maybe have an external disk where we can store backups Virtualization: we need to be able to setup few servers for development. The scenario is something like this (~8 appliances running in parallel): Redmine + GIT server Bacula server FTP server 3-4 virtual appliances that could be set up on demand to test our applications or support a customer. The appliances could be: LAMP, Tomcat+PostgreSQL, SQL Server Support: if something breaks down it shouldn't be too difficult to find a replacement. Now, given the main requirements, there are some doubts we need to clarify: Do you suggest to buy a prepackaged solution (for example a customized Dell PowerEdge T110 or T310) or to assemble the server by ourselves (buy the separate components)? What RAID configuration do you suggest? I was thinking of RAID1 (probably cheaper) or RAID5. should we buy a hardware RAID controller or is it ok to use a software RAID (mdadm)? In case, which controller do you suggest? What processor do you suggest (Intel Xeon, i3, i5, i7, AMD)? How much RAM? (I was thinking at least 8GB, ~1GB per appliance) What virtualization software do you recommend? VMWare seems to be the best choice, but what about XEN or KVM? We don't want to buy licenses at the moment so we would like to consider only free options. What OS do you recommend? We know Ubuntu, Debian, Gentoo very well (we would like to use Ubuntu Server), however it seems a lot of people goes for CentOS. Thanks in advance if you can help us with this! It's our first "serious" server so many doubts popped up :) Please feel free to add further recommendations if you have some to share ;) Have a nice day

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• Installing Lubuntu 14.04.1 fails, upowerd appears to hang

  - by Rantanplan

  On the live-CD session, I tried installing Lubuntu double clicking on the install button on the desktop. Here, the CD starts running but then stops running and nothing happens. Next, I rebooted and tried installing Lubuntu directly from the boot menu screen using forcepae again. After a while, I receive the following error message: The installer encountered an unrecoverable error. A desktop session will now be run so that you may investigate the problem or try installing again. Hitting Enter brings me to the desktop. For what errors should I search? And how? Thanks for some hints! On Lubuntu 12.04: uname -a Linux humboldt 3.2.0-67-generic #101-Ubuntu SMP Tue Jul 15 17:45:51 UTC 2014 i686 i686 i386 GNU/Linux lsb_release -a No LSB modules are available. Distributor ID: Ubuntu Description: Ubuntu 12.04.5 LTS Release: 12.04 Codename: precise upowerd appears to hang: Aug 25 10:53:28 lubuntu kernel: [ 367.920272] INFO: task upowerd:3002 blocked for more than 120 seconds. Aug 25 10:53:28 lubuntu kernel: [ 367.920288] Tainted: G S C 3.13.0-32-generic #57-Ubuntu Aug 25 10:53:28 lubuntu kernel: [ 367.920294] "echo 0 > /proc/sys/kernel/hung_task_timeout_secs" disables this message. Aug 25 10:53:28 lubuntu kernel: [ 367.920300] upowerd D e21f9da0 0 3002 1 0x00000000 Aug 25 10:53:28 lubuntu kernel: [ 367.920314] e21f9dfc 00000086 f5ef7094 e21f9da0 c1050272 c1a8d540 c1920a00 00000000 Aug 25 10:53:28 lubuntu kernel: [ 367.920333] c1a8d540 c1920a00 d9e44da0 f5ef6540 c1129061 00000002 000001c1 0001c37b Aug 25 10:53:28 lubuntu kernel: [ 367.920351] 00000000 00000002 00000000 e2276240 00000000 00000040 c12b0ec5 c19975a8 Aug 25 10:53:28 lubuntu kernel: [ 367.920368] Call Trace: Aug 25 10:53:28 lubuntu kernel: [ 367.920389] [<c1050272>] ? kmap_atomic_prot+0x42/0x100 Aug 25 10:53:28 lubuntu kernel: [ 367.920404] [<c1129061>] ? get_page_from_freelist+0x2a1/0x600 Aug 25 10:53:28 lubuntu kernel: [ 367.920417] [<c12b0ec5>] ? process_measurement+0x65/0x240 Aug 25 10:53:28 lubuntu kernel: [ 367.920432] [<c1654c73>] schedule_preempt_disabled+0x23/0x60 Aug 25 10:53:28 lubuntu kernel: [ 367.920443] [<c16565bd>] __mutex_lock_slowpath+0x10d/0x171 Aug 25 10:53:28 lubuntu kernel: [ 367.920454] [<c1655aec>] mutex_lock+0x1c/0x28 Aug 25 10:53:28 lubuntu kernel: [ 367.920478] [<f857223a>] acpi_smbus_transaction+0x48/0x210 [sbshc] Aug 25 10:53:28 lubuntu kernel: [ 367.920489] [<c11858e1>] ? do_last+0x1b1/0xf60 Aug 25 10:53:28 lubuntu kernel: [ 367.920504] [<f857242f>] acpi_smbus_read+0x2d/0x33 [sbshc] Aug 25 10:53:28 lubuntu kernel: [ 367.920520] [<f881e0f1>] acpi_battery_get_state+0x74/0x8b [sbs] Aug 25 10:53:28 lubuntu kernel: [ 367.920535] [<f881e8a9>] acpi_sbs_battery_get_property+0x2a/0x233 [sbs] Aug 25 10:53:28 lubuntu kernel: [ 367.920549] [<c14fa61f>] power_supply_show_property+0x3f/0x240 Aug 25 10:53:28 lubuntu kernel: [ 367.920561] [<c114664f>] ? handle_mm_fault+0x64f/0x8d0 Aug 25 10:53:28 lubuntu kernel: [ 367.920573] [<c14fa5e0>] ? power_supply_store_property+0x60/0x60 Aug 25 10:53:28 lubuntu kernel: [ 367.920586] [<c1407d20>] ? dev_uevent_name+0x30/0x30 Aug 25 10:53:28 lubuntu kernel: [ 367.920597] [<c1407d38>] dev_attr_show+0x18/0x40 Aug 25 10:53:28 lubuntu kernel: [ 367.920608] [<c11dad15>] sysfs_seq_show+0xe5/0x1c0 Aug 25 10:53:28 lubuntu kernel: [ 367.920621] [<c119846e>] seq_read+0xce/0x370 Aug 25 10:53:28 lubuntu kernel: [ 367.920633] [<c11983a0>] ? seq_hlist_next_percpu+0x90/0x90 Aug 25 10:53:28 lubuntu kernel: [ 367.920644] [<c1179238>] vfs_read+0x78/0x140 Aug 25 10:53:28 lubuntu kernel: [ 367.920654] [<c11799a9>] SyS_read+0x49/0x90 Aug 25 10:53:28 lubuntu kernel: [ 367.920667] [<c165efcd>] sysenter_do_call+0x12/0x28 /var/log/installer/debug shows upower related error: Ubiquity 2.18.8 Gtk-Message: Failed to load module "overlay-scrollbar" Gtk-Message: Failed to load module "overlay-scrollbar" ERROR:dbus.proxies:Introspect error on :1.23:/org/freedesktop/UPower: dbus.exceptions.DBusException: org.freedesktop.DBus.Error.NoReply: Did not receive a reply. Possible causes include: the remote application did not send a reply, the message bus security policy blocked the reply, the reply timeout expired, or the network connection was broken. Exception in GTK frontend (invoking crash handler): Traceback (most recent call last): File "/usr/lib/ubiquity/bin/ubiquity", line 636, in <module> main(oem_config) File "/usr/lib/ubiquity/bin/ubiquity", line 622, in main install(query=options.query) File "/usr/lib/ubiquity/bin/ubiquity", line 260, in install wizard = ui.Wizard(distro) File "/usr/lib/ubiquity/ubiquity/frontend/gtk_ui.py", line 290, in __init__ mod.ui = mod.ui_class(mod.controller) File "/usr/lib/ubiquity/plugins/ubi-prepare.py", line 93, in __init__ upower.setup_power_watch(self.prepare_power_source) File "/usr/lib/ubiquity/ubiquity/upower.py", line 21, in setup_power_watch power_state_changed() File "/usr/lib/ubiquity/ubiquity/upower.py", line 18, in power_state_changed not misc.get_prop(upower, UPOWER_PATH, 'OnBattery')) File "/usr/lib/ubiquity/ubiquity/misc.py", line 809, in get_prop return obj.Get(iface, prop, dbus_interface=dbus.PROPERTIES_IFACE) File "/usr/lib/python3/dist-packages/dbus/proxies.py", line 70, in __call__ return self._proxy_method(*args, **keywords) File "/usr/lib/python3/dist-packages/dbus/proxies.py", line 145, in __call__ **keywords) File "/usr/lib/python3/dist-packages/dbus/connection.py", line 651, in call_blocking message, timeout)

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• jenkins-maven-android when running throwing the error "android-sdk-linux/platforms" is not a directory"

  - by Sam

  I start setting up the jenkins-maven-android and i'm facing an issue when running the jenkin job. My Machine Details $uname -a Linux development2 3.0.0-12-virtual #20-Ubuntu SMP Fri Oct 7 18:19:02 UTC 2011 x86_64 x86_64 x86_64 GNU/Linux Steps to install the Android SDK in Ubuntu https://help.ubuntu.com/community/AndroidSDK since i'm working on headless env (ssh to client machine) i used following command to install the platform tools android update sdk --no-ui download apache maven and install on http://maven.apache.org/download.html mvn -version output root@development2:/opt/android-sdk-linux/tools# mvn -version Apache Maven 3.0.4 (r1232337; 2012-01-17 08:44:56+0000) Maven home: /opt/apache-maven-3.0.4 Java version: 1.6.0_24, vendor: Sun Microsystems Inc. Java home: /usr/lib/jvm/java-6-openjdk/jre Default locale: en_US, platform encoding: UTF-8 OS name: "linux", version: "3.0.0-12-virtual", arch: "amd64", family: "unix" root@development2:/opt/android-sdk-linux/tools# ran the following two command as mention in below sudo apt-get update sudo apt-get install ia32-libs Problems with Eclipse and Android SDK http://developer.android.com/sdk/installing/index.html As error suggest i gave the path to android SDK in jenkins build config still im getting the error clean install -Dandroid.sdk.path=/opt/android-sdk-linux Can someone help me to resolve this. Thanks Error I'm Getting Waiting for Jenkins to finish collecting data mavenExecutionResult exceptions not empty message : Failed to execute goal com.jayway.maven.plugins.android.generation2:android-maven-plugin:3.1.1:generate-sources (default-generate-sources) on project base-template: Execution default-generate-sources of goal com.jayway.maven.plugins.android.generation2:android-maven-plugin:3.1.1:generate-sources failed: Path "/opt/android-sdk-linux/platforms" is not a directory. Please provide a proper Android SDK directory path as configuration parameter <sdk><path>...</path></sdk> in the plugin <configuration/>. As an alternative, you may add the parameter to commandline: -Dandroid.sdk.path=... or set environment variable ANDROID_HOME. cause : Execution default-generate-sources of goal com.jayway.maven.plugins.android.generation2:android-maven-plugin:3.1.1:generate-sources failed: Path "/opt/android-sdk-linux/platforms" is not a directory. Please provide a proper Android SDK directory path as configuration parameter <sdk><path>...</path></sdk> in the plugin <configuration/>. As an alternative, you may add the parameter to commandline: -Dandroid.sdk.path=... or set environment variable ANDROID_HOME. Stack trace : org.apache.maven.lifecycle.LifecycleExecutionException: Failed to execute goal com.jayway.maven.plugins.android.generation2:android-maven-plugin:3.1.1:generate-sources (default-generate-sources) on project base-template: Execution default-generate-sources of goal com.jayway.maven.plugins.android.generation2:android-maven-plugin:3.1.1:generate-sources failed: Path "/opt/android-sdk-linux/platforms" is not a directory. Please provide a proper Android SDK directory path as configuration parameter <sdk><path>...</path></sdk> in the plugin <configuration/>. As an alternative, you may add the parameter to commandline: -Dandroid.sdk.path=... or set environment variable ANDROID_HOME. at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:225) at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:153) at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:145) at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject(LifecycleModuleBuilder.java:84) at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject(LifecycleModuleBuilder.java:59) at org.apache.maven.lifecycle.internal.LifecycleStarter.singleThreadedBuild(LifecycleStarter.java:183) at org.apache.maven.lifecycle.internal.LifecycleStarter.execute(LifecycleStarter.java:161) at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:320) at org.apache.maven.DefaultMaven.execute(DefaultMaven.java:156) at org.jvnet.hudson.maven3.launcher.Maven3Launcher.main(Maven3Launcher.java:79) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:616) at org.codehaus.plexus.classworlds.launcher.Launcher.launchStandard(Launcher.java:329) at org.codehaus.plexus.classworlds.launcher.Launcher.launch(Launcher.java:239) at org.jvnet.hudson.maven3.agent.Maven3Main.launch(Maven3Main.java:158) at hudson.maven.Maven3Builder.call(Maven3Builder.java:98) at hudson.maven.Maven3Builder.call(Maven3Builder.java:64) at hudson.remoting.UserRequest.perform(UserRequest.java:118) at hudson.remoting.UserRequest.perform(UserRequest.java:48) at hudson.remoting.Request$2.run(Request.java:326) at hudson.remoting.InterceptingExecutorService$1.call(InterceptingExecutorService.java:72) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334) at java.util.concurrent.FutureTask.run(FutureTask.java:166) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1110) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:603) at java.lang.Thread.run(Thread.java:679) Caused by: org.apache.maven.plugin.PluginExecutionException: Execution default-generate-sources of goal com.jayway.maven.plugins.android.generation2:android-maven-plugin:3.1.1:generate-sources failed: Path "/opt/android-sdk-linux/platforms" is not a directory. Please provide a proper Android SDK directory path as configuration parameter <sdk><path>...</path></sdk> in the plugin <configuration/>. As an alternative, you may add the parameter to commandline: -Dandroid.sdk.path=... or set environment variable ANDROID_HOME. at org.apache.maven.plugin.DefaultBuildPluginManager.executeMojo(DefaultBuildPluginManager.java:110) at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:209) ... 27 more Caused by: com.jayway.maven.plugins.android.InvalidSdkException: Path "/opt/android-sdk-linux/platforms" is not a directory. Please provide a proper Android SDK directory path as configuration parameter <sdk><path>...</path></sdk> in the plugin <configuration/>. As an alternative, you may add the parameter to commandline: -Dandroid.sdk.path=... or set environment variable ANDROID_HOME. at com.jayway.maven.plugins.android.AndroidSdk.assertPathIsDirectory(AndroidSdk.java:125) at com.jayway.maven.plugins.android.AndroidSdk.getPlatformDirectories(AndroidSdk.java:285) at com.jayway.maven.plugins.android.AndroidSdk.findAvailablePlatforms(AndroidSdk.java:260) at com.jayway.maven.plugins.android.AndroidSdk.<init>(AndroidSdk.java:80) at com.jayway.maven.plugins.android.AbstractAndroidMojo.getAndroidSdk(AbstractAndroidMojo.java:844) at com.jayway.maven.plugins.android.phase01generatesources.GenerateSourcesMojo.generateR(GenerateSourcesMojo.java:329) at com.jayway.maven.plugins.android.phase01generatesources.GenerateSourcesMojo.execute(GenerateSourcesMojo.java:102) at org.apache.maven.plugin.DefaultBuildPluginManager.executeMojo(DefaultBuildPluginManager.java:101) ... 28 more channel stopped Finished: FAILURE* android home Echo root@development2:~# echo $ANDROID_HOME /opt/android-sdk-linux

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• Java Logger API

  - by Koppar

  This is a more like a tip rather than technical write up and serves as a quick intro for newbies. The logger API helps to diagnose application level or JDK level issues at runtime. There are 7 levels which decide the detailing in logging (SEVERE, WARNING, INFO, CONFIG, FINE, FINER, FINEST). Its best to start with highest level and as we narrow down, use more detailed logging for a specific area. SEVERE is the highest and FINEST is the lowest. This may not make sense until we understand some jargon. The Logger class provides the ability to stream messages to an output stream in a format that can be controlled by the user. What this translates to is, I can create a logger with this simple invocation and use it add debug messages in my class: import java.util.logging.*; private static final Logger focusLog = Logger.getLogger("java.awt.focus.KeyboardFocusManager"); if (focusLog.isLoggable(Level.FINEST)) { focusLog.log(Level.FINEST, "Calling peer setCurrentFocusOwner}); LogManager acts like a book keeper and all the getLogger calls are forwarded to LogManager. The LogManager itself is a singleton class object which gets statically initialized on JVM start up. More on this later. If there is no existing logger with the given name, a new one is created. If there is one (and not yet GC’ed), then the existing Logger object is returned. By default, a root logger is created on JVM start up. All anonymous loggers are made as the children of the root logger. Named loggers have the hierarchy as per their name resolutions. Eg: java.awt.focus is the parent logger for java.awt.focus.KeyboardFocusManager etc. Before logging any message, the logger checks for the log level specified. If null is specified, the log level of the parent logger will be set. However, if the log level is off, no log messages would be written, irrespective of the parent’s log level. All the messages that are posted to the Logger are handled as a LogRecord object.i.e. FocusLog.log would create a new LogRecord object with the log level and message as its data members). The level of logging and thread number are also tracked. LogRecord is passed on to all the registered Handlers. Handler is basically a means to output the messages. The output may be redirected to either a log file or console or a network logging service. The Handler classes use the LogManager properties to set filters and formatters. During initialization or JVM start up, LogManager looks for logging.properties file in jre/lib and sets the properties if the file is provided. An alternate location for properties file can also be specified by setting java.util.logging.config.file system property. This can be set in Java Control Panel ? Java ? Runtime parameters as -Djava.util.logging.config.file = <mylogfile> or passed as a command line parameter java -Djava.util.logging.config.file = C:/Sunita/myLog The redirection of logging depends on what is specified rather registered as a handler with JVM in the properties file. java.util.logging.ConsoleHandler sends the output to system.err and java.util.logging.FileHandler sends the output to file. File name of the log file can also be specified. If you prefer XML format output, in the configuration file, set java.util.logging.FileHandler.formatter = java.util.logging.XMLFormatter and if you prefer simple text, set set java.util.logging.FileHandler.formatter =java.util.logging.SimpleFormatter Below is the default logging Configuration file: ############################################################ # Default Logging Configuration File # You can use a different file by specifying a filename # with the java.util.logging.config.file system property. # For example java -Djava.util.logging.config.file=myfile ############################################################ ############################################################ # Global properties ############################################################ # "handlers" specifies a comma separated list of log Handler # classes. These handlers will be installed during VM startup. # Note that these classes must be on the system classpath. # By default we only configure a ConsoleHandler, which will only # show messages at the INFO and above levels. handlers= java.util.logging.ConsoleHandler # To also add the FileHandler, use the following line instead. #handlers= java.util.logging.FileHandler, java.util.logging.ConsoleHandler # Default global logging level. # This specifies which kinds of events are logged across # all loggers. For any given facility this global level # can be overriden by a facility specific level # Note that the ConsoleHandler also has a separate level # setting to limit messages printed to the console. .level= INFO ############################################################ # Handler specific properties. # Describes specific configuration info for Handlers. ############################################################ # default file output is in user's home directory. java.util.logging.FileHandler.pattern = %h/java%u.log java.util.logging.FileHandler.limit = 50000 java.util.logging.FileHandler.count = 1 java.util.logging.FileHandler.formatter = java.util.logging.XMLFormatter # Limit the message that are printed on the console to INFO and above. java.util.logging.ConsoleHandler.level = INFO java.util.logging.ConsoleHandler.formatter = java.util.logging.SimpleFormatter ############################################################ # Facility specific properties. # Provides extra control for each logger. ############################################################ # For example, set the com.xyz.foo logger to only log SEVERE # messages: com.xyz.foo.level = SEVERE Since I primarily use this method to track focus issues, here is how I get detailed awt focus related logging. Just set the logger name to java.awt.focus.level=FINEST and change the default log level to FINEST. Below is a basic sample program. The sample programs are from http://www2.cs.uic.edu/~sloan/CLASSES/java/ and have been modified to illustrate the logging API. By changing the .level property in the logging.properties file, one can control the output written to the logs. To play around with the example, try changing the levels in the logging.properties file and notice the difference in messages going to the log file. Example --------KeyboardReader.java------------------------------------------------------------------------------------- import java.io.*; import java.util.*; import java.util.logging.*; public class KeyboardReader { private static final Logger mylog = Logger.getLogger("samples.input"); public static void main (String[] args) throws java.io.IOException { String s1; String s2; double num1, num2, product; // set up the buffered reader to read from the keyboard BufferedReader br = new BufferedReader (new InputStreamReader (System.in)); System.out.println ("Enter a line of input"); s1 = br.readLine(); if (mylog.isLoggable(Level.SEVERE)) { mylog.log (Level.SEVERE,"The line entered is " + s1); } if (mylog.isLoggable(Level.INFO)) { mylog.log (Level.INFO,"The line has " + s1.length() + " characters"); } if (mylog.isLoggable(Level.FINE)) { mylog.log (Level.FINE,"Breaking the line into tokens we get:"); } int numTokens = 0; StringTokenizer st = new StringTokenizer (s1); while (st.hasMoreTokens()) { s2 = st.nextToken(); numTokens++; if (mylog.isLoggable(Level.FINEST)) { mylog.log (Level.FINEST, " Token " + numTokens + " is: " + s2); } } } } ----------MyFileReader.java---------------------------------------------------------------------------------------- import java.io.*; import java.util.*; import java.util.logging.*; public class MyFileReader extends KeyboardReader { private static final Logger mylog = Logger.getLogger("samples.input.file"); public static void main (String[] args) throws java.io.IOException { String s1; String s2; // set up the buffered reader to read from the keyboard BufferedReader br = new BufferedReader (new FileReader ("MyFileReader.txt")); s1 = br.readLine(); if (mylog.isLoggable(Level.SEVERE)) { mylog.log (Level.SEVERE,"ATTN The line is " + s1); } if (mylog.isLoggable(Level.INFO)) { mylog.log (Level.INFO, "The line has " + s1.length() + " characters"); } if (mylog.isLoggable(Level.FINE)) { mylog.log (Level.FINE,"Breaking the line into tokens we get:"); } int numTokens = 0; StringTokenizer st = new StringTokenizer (s1); while (st.hasMoreTokens()) { s2 = st.nextToken(); numTokens++; if (mylog.isLoggable(Level.FINEST)) { mylog.log (Level.FINEST,"Breaking the line into tokens we get:"); mylog.log (Level.FINEST," Token " + numTokens + " is: " + s2); } } //end of while } // end of main } // end of class ----------MyFileReader.txt------------------------------------------------------------------------------------------ My first logging example -------logging.properties------------------------------------------------------------------------------------------- handlers= java.util.logging.ConsoleHandler, java.util.logging.FileHandler .level= FINEST java.util.logging.FileHandler.pattern = java%u.log java.util.logging.FileHandler.limit = 50000 java.util.logging.FileHandler.count = 1 java.util.logging.FileHandler.formatter = java.util.logging.SimpleFormatter java.util.logging.ConsoleHandler.level = FINEST java.util.logging.ConsoleHandler.formatter = java.util.logging.SimpleFormatter java.awt.focus.level=ALL ------Output log------------------------------------------------------------------------------------------- May 21, 2012 11:44:55 AM MyFileReader main SEVERE: ATTN The line is My first logging example May 21, 2012 11:44:55 AM MyFileReader main INFO: The line has 24 characters May 21, 2012 11:44:55 AM MyFileReader main FINE: Breaking the line into tokens we get: May 21, 2012 11:44:55 AM MyFileReader main FINEST: Breaking the line into tokens we get: May 21, 2012 11:44:55 AM MyFileReader main FINEST: Token 1 is: My May 21, 2012 11:44:55 AM MyFileReader main FINEST: Breaking the line into tokens we get: May 21, 2012 11:44:55 AM MyFileReader main FINEST: Token 2 is: first May 21, 2012 11:44:55 AM MyFileReader main FINEST: Breaking the line into tokens we get: May 21, 2012 11:44:55 AM MyFileReader main FINEST: Token 3 is: logging May 21, 2012 11:44:55 AM MyFileReader main FINEST: Breaking the line into tokens we get: May 21, 2012 11:44:55 AM MyFileReader main FINEST: Token 4 is: example Invocation command: "C:\Program Files (x86)\Java\jdk1.6.0_29\bin\java.exe" -Djava.util.logging.config.file=logging.properties MyFileReader References Further technical details are available here: http://docs.oracle.com/javase/1.4.2/docs/guide/util/logging/overview.html#1.0 http://docs.oracle.com/javase/1.4.2/docs/api/java/util/logging/package-summary.html http://www2.cs.uic.edu/~sloan/CLASSES/java/

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• Your thoughts on Best Practices for Scientific Computing?

  - by John Smith

  A recent paper by Wilson et al (2014) pointed out 24 Best Practices for scientific programming. It's worth to have a look. I would like to hear opinions about these points from experienced programmers in scientific data analysis. Do you think these advices are helpful and practical? Or are they good only in an ideal world? Wilson G, Aruliah DA, Brown CT, Chue Hong NP, Davis M, Guy RT, Haddock SHD, Huff KD, Mitchell IM, Plumbley MD, Waugh B, White EP, Wilson P (2014) Best Practices for Scientific Computing. PLoS Biol 12:e1001745. http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001745 Box 1. Summary of Best Practices Write programs for people, not computers. (a) A program should not require its readers to hold more than a handful of facts in memory at once. (b) Make names consistent, distinctive, and meaningful. (c) Make code style and formatting consistent. Let the computer do the work. (a) Make the computer repeat tasks. (b) Save recent commands in a file for re-use. (c) Use a build tool to automate workflows. Make incremental changes. (a) Work in small steps with frequent feedback and course correction. (b) Use a version control system. (c) Put everything that has been created manually in version control. Don’t repeat yourself (or others). (a) Every piece of data must have a single authoritative representation in the system. (b) Modularize code rather than copying and pasting. (c) Re-use code instead of rewriting it. Plan for mistakes. (a) Add assertions to programs to check their operation. (b) Use an off-the-shelf unit testing library. (c) Turn bugs into test cases. (d) Use a symbolic debugger. Optimize software only after it works correctly. (a) Use a profiler to identify bottlenecks. (b) Write code in the highest-level language possible. Document design and purpose, not mechanics. (a) Document interfaces and reasons, not implementations. (b) Refactor code in preference to explaining how it works. (c) Embed the documentation for a piece of software in that software. Collaborate. (a) Use pre-merge code reviews. (b) Use pair programming when bringing someone new up to speed and when tackling particularly tricky problems. (c) Use an issue tracking tool. I'm relatively new to serious programming for scientific data analysis. When I tried to write code for pilot analyses of some of my data last year, I encountered tremendous amount of bugs both in my code and data. Bugs and errors had been around me all the time, but this time it was somewhat overwhelming. I managed to crunch the numbers at last, but I thought I couldn't put up with this mess any longer. Some actions must be taken. Without a sophisticated guide like the article above, I started to adopt "defensive style" of programming since then. A book titled "The Art of Readable Code" helped me a lot. I deployed meticulous input validations or assertions for every function, renamed a lot of variables and functions for better readability, and extracted many subroutines as reusable functions. Recently, I introduced Git and SourceTree for version control. At the moment, because my co-workers are much more reluctant about these issues, the collaboration practices (8a,b,c) have not been introduced. Actually, as the authors admitted, because all of these practices take some amount of time and effort to introduce, it may be generally hard to persuade your reluctant collaborators to comply them. I think I'm asking your opinions because I still suffer from many bugs despite all my effort on many of these practices. Bug fix may be, or should be, faster than before, but I couldn't really measure the improvement. Moreover, much of my time has been invested on defence, meaning that I haven't actually done much data analysis (offence) these days. Where is the point I should stop at in terms of productivity? I've already deployed: 1a,b,c, 2a, 3a,b,c, 4b,c, 5a,d, 6a,b, 7a,7b I'm about to have a go at: 5b,c Not yet: 2b,c, 4a, 7c, 8a,b,c (I could not really see the advantage of using GNU make (2c) for my purpose. Could anyone tell me how it helps my work with MATLAB?)

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• System locking up with suspicious messages about hard disk

  - by Chris Conway

  My system has started behaving strangely, intermittently locking up. I see messages like the following in syslog: Nov 18 22:22:00 claypool kernel: [ 3428.078156] ata3.00: exception Emask 0x0 SAct 0x0 SErr 0x0 action 0x0 Nov 18 22:22:00 claypool kernel: [ 3428.078163] ata3.00: irq_stat 0x40000000 Nov 18 22:22:00 claypool kernel: [ 3428.078167] sr 2:0:0:0: CDB: Test Unit Ready: 00 00 00 00 00 00 Nov 18 22:22:00 claypool kernel: [ 3428.078182] ata3.00: cmd a0/00:00:00:00:00/00:00:00:00:00/a0 tag 0 Nov 18 22:22:00 claypool kernel: [ 3428.078184] res 50/00:03:00:00:00/00:00:00:00:00/a0 Emask 0x1 (device error) Nov 18 22:22:00 claypool kernel: [ 3428.078188] ata3.00: status: { DRDY } Nov 18 22:22:00 claypool kernel: [ 3428.080887] ata3.00: exception Emask 0x0 SAct 0x0 SErr 0x0 action 0x0 Nov 18 22:22:00 claypool kernel: [ 3428.080890] ata3.00: irq_stat 0x40000000 Nov 18 22:22:00 claypool kernel: [ 3428.080893] sr 2:0:0:0: CDB: Test Unit Ready: 00 00 00 00 00 00 Nov 18 22:22:00 claypool kernel: [ 3428.080905] ata3.00: cmd a0/00:00:00:00:00/00:00:00:00:00/a0 tag 0 Nov 18 22:22:00 claypool kernel: [ 3428.080906] res 50/00:03:00:00:00/00:00:00:00:00/a0 Emask 0x1 (device error) Nov 18 22:22:00 claypool kernel: [ 3428.080910] ata3.00: status: { DRDY } And then this: Nov 18 23:13:56 claypool kernel: [ 6544.000798] ata1.00: exception Emask 0x0 SAct 0x0 SErr 0x0 action 0x6 frozen Nov 18 23:13:56 claypool kernel: [ 6544.000804] ata1.00: failed command: FLUSH CACHE EXT Nov 18 23:13:56 claypool kernel: [ 6544.000814] ata1.00: cmd ea/00:00:00:00:00/00:00:00:00:00/a0 tag 0 Nov 18 23:13:56 claypool kernel: [ 6544.000815] res 40/00:00:00:4f:c2/00:00:00:00:00/40 Emask 0x4 (timeout) Nov 18 23:13:56 claypool kernel: [ 6544.000819] ata1.00: status: { DRDY } Nov 18 23:13:56 claypool kernel: [ 6544.000825] ata1: hard resetting link Nov 18 23:14:01 claypool kernel: [ 6549.360324] ata1: link is slow to respond, please be patient (ready=0) Nov 18 23:14:06 claypool kernel: [ 6554.008091] ata1: COMRESET failed (errno=-16) Nov 18 23:14:06 claypool kernel: [ 6554.008103] ata1: hard resetting link Nov 18 23:14:11 claypool kernel: [ 6559.372246] ata1: link is slow to respond, please be patient (ready=0) Nov 18 23:14:16 claypool kernel: [ 6564.020228] ata1: COMRESET failed (errno=-16) Nov 18 23:14:16 claypool kernel: [ 6564.020235] ata1: hard resetting link Nov 18 23:14:21 claypool kernel: [ 6569.380109] ata1: link is slow to respond, please be patient (ready=0) Nov 18 23:14:31 claypool kernel: [ 6579.460243] ata1: SATA link up 3.0 Gbps (SStatus 123 SControl 300) Nov 18 23:14:31 claypool kernel: [ 6579.486595] ata1.00: configured for UDMA/133 Nov 18 23:14:31 claypool kernel: [ 6579.486601] ata1.00: retrying FLUSH 0xea Emask 0x4 Nov 18 23:14:31 claypool kernel: [ 6579.486939] ata1.00: device reported invalid CHS sector 0 Nov 18 23:14:31 claypool kernel: [ 6579.486952] ata1: EH complete Nov 18 23:17:01 claypool CRON[3910]: (root) CMD ( cd / && run-parts --report /etc/cron.hourly) Nov 18 23:17:01 claypool CRON[3908]: (CRON) error (grandchild #3910 failed with exit status 1) Nov 18 23:17:01 claypool postfix/sendmail[3925]: fatal: open /etc/postfix/main.cf: No such file or directory Nov 18 23:17:01 claypool CRON[3908]: (root) MAIL (mailed 1 byte of output; but got status 0x004b, #012) Nov 18 23:39:01 claypool CRON[4200]: (root) CMD ( [ -x /usr/lib/php5/maxlifetime ] && [ -d /var/lib/php5 ] && find /var/lib/php5/ -type f -cmin +$(/usr/lib/php5/maxlifetime) -print0 | xargs -n 200 -r -0 rm) There are no messages marked after 23:39. When I next tried to use the machine, it would not return from the screensaver (blank screen), nor switch to another terminal, and I had to hard reboot it. [UPDATE] The output of smartctl is here. I had trouble getting this, because / is being mounted read-only (?!), which prevents most applications from running. Also, it may not be related, but I have the following worrying messages in dmesg: [ 10.084596] k8temp 0000:00:18.3: Temperature readouts might be wrong - check erratum #141 [ 10.098477] i2c i2c-0: nForce2 SMBus adapter at 0x600 [ 10.098483] ACPI: resource nForce2_smbus [io 0x0700-0x073f] conflicts with ACPI region SM00 [??? 0x00000700-0x0000073f flags 0x30] [ 10.098486] ACPI: This conflict may cause random problems and system instability [ 10.098487] ACPI: If an ACPI driver is available for this device, you should use it instead of the native driver [ 10.098509] i2c i2c-1: nForce2 SMBus adapter at 0x700 [ 10.112570] Linux agpgart interface v0.103 [ 10.155329] atk: Resources not safely usable due to acpi_enforce_resources kernel parameter [ 10.161506] it87: Found IT8712F chip at 0x290, revision 8 [ 10.161517] it87: VID is disabled (pins used for GPIO) [ 10.161527] it87: in3 is VCC (+5V) [ 10.161528] it87: in7 is VCCH (+5V Stand-By) [ 10.161560] ACPI: resource it87 [io 0x0295-0x0296] conflicts with ACPI region ECRE [??? 0x00000290-0x000002af flags 0x45] [ 10.161562] ACPI: This conflict may cause random problems and system instability [ 10.161564] ACPI: If an ACPI driver is available for this device, you should use it instead of the native driver [UPDATE 2] I swapped in a new SATA cable, per Phil's suggestion. The current output of smartctl is here, if it helps. [UPDATE 3] I don't think the cable fixed it. The system hasn't locked up yet, but my media player crashed a few minutes ago and I have the following in the syslog: Nov 20 16:07:17 claypool kernel: [ 2294.400033] ata1: link is slow to respond, please be patient (ready=0) Nov 20 16:07:47 claypool kernel: [ 2324.084581] ata1: COMRESET failed (errno=-16) Nov 20 16:07:47 claypool kernel: [ 2324.084588] ata1: limiting SATA link speed to 1.5 Gbps Nov 20 16:07:47 claypool kernel: [ 2324.084592] ata1: hard resetting link I get the following response from smartctl: $ sudo smartctl -a /dev/sda [sudo] password for chris: sudo: Can't open /var/lib/sudo/chris/0: Read-only file system smartctl 5.40 2010-03-16 r3077 [i686-pc-linux-gnu] (local build) Copyright (C) 2002-10 by Bruce Allen, http://smartmontools.sourceforge.net Device: /0:0:0:0 Version: scsiModePageOffset: response length too short, resp_len=47 offset=50 bd_len=46 >> Terminate command early due to bad response to IEC mode page A mandatory SMART command failed: exiting. To continue, add one or more '-T permissive' options.

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