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  • CMake and BLAS for a C program

    - by SuperBloup
    I'm trying to use CMake to build a program relying on blas, I'm detecting blas using : include (${CMAKE_ROOT}/Modules/FindBLAS.cmake) The problem is, FindBLAS require a fortran compiler and complain with -- Looking for BLAS... - NOT found (Fortran not enabled) As blas is already installed on my machine (ATLAS Blas), and gfortran is also installed, how can I enable Fortran, or is there a workaround to find the blas library for C?

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  • oprofile unable to produce call graph

    - by aaa
    hello I am trying to use oprofile to generate call graph. Compiler is g++, platform is linux x86-64, linker is gfortran C++ code is compiled with -fno- omit-frame-pointer. oprofile is started with --callgraph=25. report I run with --callgraph. the call graph is produced but it's only includes self time, which is not much use what am I missing?

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  • How do I tell if a Python pip install is working correctly or hanging?

    - by wobbily_col
    I am trying to install the python pandas package in a virtualenv using pip. On my development machine it installed correctly, but now I am trying on the server, it gets so far then it seems to get stuck: warnings.warn(LapackSrcNotFoundError.__doc__) /apps/PYTHON/2.7.3/lib/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: 'define_macros' warnings.warn(msg) non-existing path in 'numpy/distutils': 'site.cfg' non-existing path in 'numpy/lib': 'benchmarks' Could not locate executable gfortran Could not locate executable f95 Found executable /apps/modules/wrappers/fortran/ifort Top shows ifort running at 46% cpu. Is there any way I can tell if this is working correctly (can I check files it is updating for example), or if it is stuck in a loop? It has been running for 40 minutes so far.

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  • How to install suggested packages in apt-get

    - by Alaa Ali
    EDIT: I solved my issue. I will answer my own question, but in 5 hours because I don't have permission now. I know the question has been asked before, but please hear me out. So I wanted to install screenlets. I ran sudo apt-get install screenlets, and this is what I got: The following extra packages will be installed: libart-2.0-2 libbonobo2-0 libbonobo2-common libbonoboui2-0 libbonoboui2-common libgnome2-0 libgnomecanvas2-0 libgnomecanvas2-common libgnomeui-0 libgnomeui-common libtidy-0.99-0 python-beautifulsoup python-evolution python-feedparser python-gmenu python-gnome2 python-numpy python-pyorbit python-rsvg python-tz python-utidylib screenlets-pack-basic Suggested packages: libbonobo2-bin python-gnome2-doc python-numpy-doc python-numpy-dbg python-nose python-dev gfortran python-pyorbit-dbg screenlets-pack-all python-dcop Recommended packages: python-numeric python-gnome2-extras The following NEW packages will be installed: libart-2.0-2 libbonobo2-0 libbonobo2-common libbonoboui2-0 libbonoboui2-common libgnome2-0 libgnomecanvas2-0 libgnomecanvas2-common libgnomeui-0 libgnomeui-common libtidy-0.99-0 python-beautifulsoup python-evolution python-feedparser python-gmenu python-gnome2 python-numpy python-pyorbit python-rsvg python-tz python-utidylib screenlets screenlets-pack-basic 0 upgraded, 23 newly installed, 0 to remove and 2 not upgraded. People say that Recommended packages are installed by default, but they are clearly not included in the NEW packages that will be installed above. I also decided to include the Suggested packages in the installation, so I ran sudo apt-get --install-suggests install screenlets instead, but I got a HUGE list of NEW packages that will be installed; that number is precisely 0 upgraded, 944 newly installed, 0 to remove and 2 not upgraded. Should'nt I be getting only around 10 extra packages?

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  • Creating Python C module from Fortran sources on Ubuntu 10.04 LTS

    - by Botondus
    In a project I work on we use a Python C module compiled from Fortran with f2py. I've had no issues building it on Windows 7 32bit (using mingw32) and on the servers it's built on 32bit Linux. But I've recently installed Ubuntu 10.04 LTS 64bit on my laptop that I use for development, and when I build it I get a lot of warnings (even though I've apparently installed all gcc/fortran libraries/compilers), but it does finish the build. However when I try to use the built module in the application, most of it seems to run well but then it crashes with an error: * glibc detected /home/botondus/Envs/gasit/bin/python: free(): invalid next size (fast): 0x0000000006a44760 ** Warnings on running *f2py -c -m module_name ./fortran/source.f90* customize UnixCCompiler customize UnixCCompiler using build_ext customize GnuFCompiler Could not locate executable g77 Found executable /usr/bin/f77 gnu: no Fortran 90 compiler found gnu: no Fortran 90 compiler found customize IntelFCompiler Could not locate executable ifort Could not locate executable ifc customize LaheyFCompiler Could not locate executable lf95 customize PGroupFCompiler Could not locate executable pgf90 Could not locate executable pgf77 customize AbsoftFCompiler Could not locate executable f90 absoft: no Fortran 90 compiler found absoft: no Fortran 90 compiler found absoft: no Fortran 90 compiler found absoft: no Fortran 90 compiler found absoft: no Fortran 90 compiler found absoft: no Fortran 90 compiler found customize NAGFCompiler Found executable /usr/bin/f95 customize VastFCompiler customize GnuFCompiler gnu: no Fortran 90 compiler found gnu: no Fortran 90 compiler found customize CompaqFCompiler Could not locate executable fort customize IntelItaniumFCompiler Could not locate executable efort Could not locate executable efc customize IntelEM64TFCompiler customize Gnu95FCompiler Found executable /usr/bin/gfortran customize Gnu95FCompiler customize Gnu95FCompiler using build_ext I have tried building a 32bit version by installing the gfortran multilib packages and running f2py with -m32 option (but with no success): f2py -c -m module_name ./fortran/source.f90 --f77flags="-m32" --f90flags="-m32" Any suggestions on what I could try to either build 32bit version or correctly build the 64bit version? Edit: It looks like it crashes right at the end of a subroutine. The 'write' executes fine... which is strange. write(6,*)'Eh=',Eh end subroutine calcolo_involucro The full backtrace is very long and I'm not sure if it's any help, but here it is: *** glibc detected *** /home/botondus/Envs/gasit/bin/python: free(): invalid next size (fast): 0x0000000007884690 *** ======= Backtrace: ========= /lib/libc.so.6(+0x775b6)[0x7fe24f8f05b6] /lib/libc.so.6(cfree+0x73)[0x7fe24f8f6e53] /usr/local/lib/python2.6/dist-packages/numpy/core/multiarray.so(+0x4183c)[0x7fe24a18183c] /home/botondus/Envs/gasit/bin/python[0x46a50d] /usr/local/lib/python2.6/dist-packages/numpy/core/multiarray.so(+0x4fbd8)[0x7fe24a18fbd8] /usr/local/lib/python2.6/dist-packages/numpy/core/multiarray.so(+0x5aded)[0x7fe24a19aded] /home/botondus/Envs/gasit/bin/python(PyEval_EvalFrameEx+0x516e)[0x4a7c5e] /home/botondus/Envs/gasit/bin/python(PyEval_EvalFrameEx+0x5a60)[0x4a8550] /home/botondus/Envs/gasit/bin/python(PyEval_EvalCodeEx+0x911)[0x4a9671] /home/botondus/Envs/gasit/bin/python[0x537620] /home/botondus/Envs/gasit/bin/python(PyObject_Call+0x47)[0x41f0c7] /home/botondus/Envs/gasit/bin/python[0x427dff] /home/botondus/Envs/gasit/bin/python(PyObject_Call+0x47)[0x41f0c7] /home/botondus/Envs/gasit/bin/python[0x477bff] /home/botondus/Envs/gasit/bin/python[0x46f47f] /home/botondus/Envs/gasit/bin/python(PyObject_Call+0x47)[0x41f0c7] /home/botondus/Envs/gasit/bin/python(PyEval_EvalFrameEx+0x4888)[0x4a7378] /home/botondus/Envs/gasit/bin/python(PyEval_EvalCodeEx+0x911)[0x4a9671] /home/botondus/Envs/gasit/bin/python(PyEval_EvalFrameEx+0x4d19)[0x4a7809] /home/botondus/Envs/gasit/bin/python(PyEval_EvalCodeEx+0x911)[0x4a9671] /home/botondus/Envs/gasit/bin/python(PyEval_EvalFrameEx+0x4d19)[0x4a7809] /home/botondus/Envs/gasit/bin/python(PyEval_EvalCodeEx+0x911)[0x4a9671] /home/botondus/Envs/gasit/bin/python[0x537620] /home/botondus/Envs/gasit/bin/python(PyObject_Call+0x47)[0x41f0c7] /home/botondus/Envs/gasit/bin/python(PyEval_CallObjectWithKeywords+0x43)[0x4a1b03] /usr/local/lib/python2.6/dist-packages/numpy/core/multiarray.so(+0x2ee94)[0x7fe24a16ee94] /home/botondus/Envs/gasit/bin/python(_PyObject_Str+0x61)[0x454a81] /home/botondus/Envs/gasit/bin/python(PyObject_Str+0xa)[0x454b3a] /home/botondus/Envs/gasit/bin/python[0x461ad3] /home/botondus/Envs/gasit/bin/python[0x46f3b3] /home/botondus/Envs/gasit/bin/python(PyObject_Call+0x47)[0x41f0c7] /home/botondus/Envs/gasit/bin/python(PyEval_EvalFrameEx+0x4888)[0x4a7378] /home/botondus/Envs/gasit/bin/python(PyEval_EvalCodeEx+0x911)[0x4a9671] /home/botondus/Envs/gasit/bin/python(PyEval_EvalFrameEx+0x4d19)[0x4a7809] /home/botondus/Envs/gasit/bin/python(PyEval_EvalFrameEx+0x5a60)[0x4a8550] ======= Memory map: ======== 00400000-0061c000 r-xp 00000000 08:05 399145 /home/botondus/Envs/gasit/bin/python 0081b000-0081c000 r--p 0021b000 08:05 399145 /home/botondus/Envs/gasit/bin/python 0081c000-0087e000 rw-p 0021c000 08:05 399145 /home/botondus/Envs/gasit/bin/python 0087e000-0088d000 rw-p 00000000 00:00 0 01877000-07a83000 rw-p 00000000 00:00 0 [heap] 7fe240000000-7fe240021000 rw-p 00000000 00:00 0 7fe240021000-7fe244000000 ---p 00000000 00:00 0 7fe247631000-7fe2476b1000 r-xp 00000000 08:03 140646 /usr/lib/libfreetype.so.6.3.22 7fe2476b1000-7fe2478b1000 ---p 00080000 08:03 140646 /usr/lib/libfreetype.so.6.3.22 7fe2478b1000-7fe2478b6000 r--p 00080000 08:03 140646 /usr/lib/libfreetype.so.6.3.22 7fe2478b6000-7fe2478b7000 rw-p 00085000 08:03 140646 /usr/lib/libfreetype.so.6.3.22 7fe2478b7000-7fe2478bb000 r-xp 00000000 08:03 263882 /usr/lib/python2.6/dist-packages/PIL/_imagingft.so 7fe2478bb000-7fe247aba000 ---p 00004000 08:03 263882 /usr/lib/python2.6/dist-packages/PIL/_imagingft.so 7fe247aba000-7fe247abb000 r--p 00003000 08:03 263882 /usr/lib/python2.6/dist-packages/PIL/_imagingft.so 7fe247abb000-7fe247abc000 rw-p 00004000 08:03 263882 /usr/lib/python2.6/dist-packages/PIL/_imagingft.so 7fe247abc000-7fe247abf000 r-xp 00000000 08:03 266773 /usr/lib/python2.6/lib-dynload/_bytesio.so 7fe247abf000-7fe247cbf000 ---p 00003000 08:03 266773 /usr/lib/python2.6/lib-dynload/_bytesio.so 7fe247cbf000-7fe247cc0000 r--p 00003000 08:03 266773 /usr/lib/python2.6/lib-dynload/_bytesio.so 7fe247cc0000-7fe247cc1000 rw-p 00004000 08:03 266773 /usr/lib/python2.6/lib-dynload/_bytesio.so 7fe247cc1000-7fe247cc5000 r-xp 00000000 08:03 266786 /usr/lib/python2.6/lib-dynload/_fileio.so 7fe247cc5000-7fe247ec4000 ---p 00004000 08:03 266786 /usr/lib/python2.6/lib-dynload/_fileio.so 7fe247ec4000-7fe247ec5000 r--p 00003000 08:03 266786 /usr/lib/python2.6/lib-dynload/_fileio.so 7fe247ec5000-7fe247ec6000 rw-p 00004000 08:03 266786 /usr/lib/python2.6/lib-dynload/_fileio.so 7fe247ec6000-7fe24800c000 r-xp 00000000 08:03 141358 /usr/lib/libxml2.so.2.7.6 7fe24800c000-7fe24820b000 ---p 00146000 08:03 141358 /usr/lib/libxml2.so.2.7.6 7fe24820b000-7fe248213000 r--p 00145000 08:03 141358 /usr/lib/libxml2.so.2.7.6 7fe248213000-7fe248215000 rw-p 0014d000 08:03 141358 /usr/lib/libxml2.so.2.7.6 7fe248215000-7fe248216000 rw-p 00000000 00:00 0 7fe248216000-7fe248229000 r-xp 00000000 08:03 140632 /usr/lib/libexslt.so.0.8.15 7fe248229000-7fe248428000 ---p 00013000 08:03 140632 /usr/lib/libexslt.so.0.8.15 7fe248428000-7fe248429000 r--p 00012000 08:03 140632 /usr/lib/libexslt.so.0.8.15 7fe248429000-7fe24842a000 rw-p 00013000 08:03 140632 /usr/lib/libexslt.so.0.8.15 7fe24842a000-7fe248464000 r-xp 00000000 08:03 141360 /usr/lib/libxslt.so.1.1.26 7fe248464000-7fe248663000 ---p 0003a000 08:03 141360 /usr/lib/libxslt.so.1.1.26 7fe248663000-7fe248664000 r--p 00039000 08:03 141360 /usr/lib/libxslt.so.1.1.26 7fe248664000-7fe248665000 rw-p 0003a000 08:03 141360 /usr/lib/libxslt.so.1.1.26 7fe248665000-7fe24876e000 r-xp 00000000 08:03 534240 /usr/local/lib/python2.6/dist-packages/lxml/etree.so 7fe24876e000-7fe24896d000 ---p 00109000 08:03 534240 /usr/local/lib/python2.6/dist-packages/lxml/etree.so 7fe24896d000-7fe24896e000 r--p 00108000 08:03 534240 /usr/local/lib/python2.6/dist-packages/lxml/etree.so 7fe24896e000-7fe248999000 rw-p 00109000 08:03 534240 /usr/local/lib/python2.6/dist-packages/lxml/etree.so 7fe248999000-7fe2489a7000 rw-p 00000000 00:00 0 7fe2489a7000-7fe2489bd000 r-xp 00000000 08:03 132934 /lib/libgcc_s.so.1

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  • Function pointer arrays in Fortran

    - by Eduardo Dobay
    I can create function pointers in Fortran 90, with code like real, external :: f and then use f as an argument to another function/subroutine. But what if I want an array of function pointers? In C I would just do double (*f[])(int); to create an array of functions returning double and taking an integer argument. I tried the most obvious, real, external, dimension(3) :: f but gfortran doesn't let me mix EXTERNAL and DIMENSION. Is there any way to do what I want? (The context for this is a program for solving a system of differential equations, so I could input the equations without having a million parameters in my subroutines.)

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  • An error which does not present itself with a debugger attached.

    - by ccook
    I am using Intel's FORTRAN compiler to compile a numerical library. The test case provided errors out within libc.so.6. When I attach Intel's debugger (IDB) the application runs through successfully. How do I debug a bug where the debugger prevents the bug? Note that the same bug arose with gfortran. I am working within OpenSUSE 11.2 x64. The error is: forrtl: severe (408): fort: (3): Subscript #1 of the array B has value -534829264 which is less than the lower bound of 1

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  • reading unformatted fortran file in matlab - which precision?

    - by Griff
    I have just written out a file: real*8 :: vol_cel real*8, dimension(256,256,256) :: dense [... some operations] open(unit=8,file=fname,form="unformatted") write(8)dense(:,:,:)/vol_cell close(8) dense and vol_cell are real*8 variables. My code to read this in in Matlab: fid = fopen(fname,'r'); mesh_raw = fread(fid,256*256*256,'double'); fclose(fid); The min and max values clearly show that it is not reading it in correctly (Min is 0 and max is a largish positive real*8). min = 3.3622e+38 max = -3.3661e+38 What precision do I need to set in Matlab to make it read in the unformatted Fortran file? A somewhat related question: This Matlab code I am using reads binary files OK but not unformatted files. Though I am generating this new data on my Mac OSX using gfortran. It doesn't recognize form="binary" so I can't do it that way. Do I need to add some library?

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  • Program crash for array copy with ifort

    - by Stefano Borini
    This program crashes with Illegal instruction: 4 on MacOSX Lion and ifort (IFORT) 12.1.0 20111011 program foo real, pointer :: a(:,:), b(:,:) allocate(a(5400, 5400)) allocate(b(5400, 3600)) a=1.0 b(:, 1:3600) = a(:, 1:3600) print *, a print *, b deallocate(a) deallocate(b) end program The same program works with gfortran. I don't see any problem. Any ideas ? Unrolling the copy and performing the explicit loop over the columns works in both compilers. Note that with allocatable instead of pointer I have no problems. The behavior is the same if the statement is either inside a module or not. I confirm the same behavior on Linux using ifort (IFORT) 12.1.3 20120130.

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  • Building ATLAS (and later Octave w/ ATLAS)

    - by David Parks
    I'm trying to set up ATLAS (so I can later compile octave with ATLAS support). If I'm correct, I still need to build this manually due to the environment specific optimizations. I do see a package for ATLAS, but it looks like it's using the cross platform generic build options (e.g. "it'll be slow"). So, running the configure script as described in the docs seems to go poorly. As a java developer I never do well at making heads or tails of errors in these build processes. Am I missing dependencies (if so is there any documentation on what I need)? allusers@vbubuntu:~/Downloads/atlas3.10.1/build_vbubuntu$ ../configure -b 64 -D c -DPentiumCPS=3000 --with-netlib-lapack-tarfile=/home/allusers/Downloads/lapack-3.5.0.tgz make: `xconfig' is up to date. ./xconfig -d s /home/allusers/Downloads/atlas3.10.1/build_vbubuntu/../ -d b /home/allusers/Downloads/atlas3.10.1/build_vbubuntu -b 64 -D c -DPentiumCPS=3000 -Si lapackref 1 OS configured as Linux (1) Assembly configured as GAS_x8664 (2) Vector ISA Extension configured as SSE3 (6,448) ERROR: enum fam=3, chip=2, mach=0 make[3]: *** [atlas_run] Error 44 make[2]: *** [IRunArchInfo_x86] Error 2 Architecture configured as Corei1 (25) ERROR: enum fam=3, chip=2, mach=0 make[3]: *** [atlas_run] Error 44 make[2]: *** [IRunArchInfo_x86] Error 2 Clock rate configured as 2350Mhz ERROR: enum fam=3, chip=2, mach=0 make[3]: *** [atlas_run] Error 44 make[2]: *** [IRunArchInfo_x86] Error 2 Maximum number of threads configured as 4 Parallel make command configured as '$(MAKE) -j 4' ERROR: enum fam=3, chip=2, mach=0 make[3]: *** [atlas_run] Error 44 make[2]: *** [IRunArchInfo_x86] Error 2 Cannot detect CPU throttling. rm -f config1.out make atlas_run atldir=/home/allusers/Downloads/atlas3.10.1/build_vbubuntu exe=xprobe_comp redir=config1.out \ args="-v 0 -o atlconf.txt -O 1 -A 25 -Si nof77 0 -V 448 -b 64 -d b /home/allusers/Downloads/atlas3.10.1/build_vbubuntu" make[1]: Entering directory `/home/allusers/Downloads/atlas3.10.1/build_vbubuntu' cd /home/allusers/Downloads/atlas3.10.1/build_vbubuntu ; ./xprobe_comp -v 0 -o atlconf.txt -O 1 -A 25 -Si nof77 0 -V 448 -b 64 -d b /home/allusers/Downloads/atlas3.10.1/build_vbubuntu > config1.out make[2]: gfortran: Command not found make[2]: *** [IRunF77Comp] Error 127 make[2]: g77: Command not found make[2]: *** [IRunF77Comp] Error 127 make[2]: f77: Command not found make[2]: *** [IRunF77Comp] Error 127 Unable to find usable compiler for F77; abortingMake sure compilers are in your path, and specify good compilers to configure (see INSTALL.txt or 'configure --help' for details)make[1]: *** [atlas_run] Error 8 make[1]: Leaving directory `/home/allusers/Downloads/atlas3.10.1/build_vbubuntu' make: *** [IRun_comp] Error 2 ERROR 512 IN SYSCMND: 'make IRun_comp args="-v 0 -o atlconf.txt -O 1 -A 25 -Si nof77 0 -V 448 -b 64"' mkdir src bin tune interfaces mkdir: cannot create directory ‘src’: File exists mkdir: cannot create directory ‘bin’: File exists mkdir: cannot create directory ‘tune’: File exists mkdir: cannot create directory ‘interfaces’: File exists make: *** [make_subdirs] Error 1 make -f Make.top startup make[1]: Entering directory `/home/allusers/Downloads/atlas3.10.1/build_vbubuntu' Make.top:1: Make.inc: No such file or directory Make.top:325: warning: overriding commands for target `/AtlasTest' Make.top:76: warning: ignoring old commands for target `/AtlasTest' make[1]: *** No rule to make target `Make.inc'. Stop. make[1]: Leaving directory `/home/allusers/Downloads/atlas3.10.1/build_vbubuntu' make: *** [startup] Error 2 mv: cannot move ‘lapack-3.5.0’ to ‘../reference/lapack-3.5.0’: Directory not empty mv: cannot stat ‘lib/Makefile’: No such file or directory ../configure: 450: ../configure: cannot create lib/Makefile: Directory nonexistent ../configure: 451: ../configure: cannot create lib/Makefile: Directory nonexistent ../configure: 452: ../configure: cannot create lib/Makefile: Directory nonexistent ../configure: 453: ../configure: cannot create lib/Makefile: Directory nonexistent ../configure: 509: ../configure: cannot create lib/Makefile: Directory nonexistent DONE configure

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  • How do I create a python module from a fortran program with f2py?

    - by Lars Hellemo
    I am trying to read some smps files with python, and found a fortran implementation, so I thought I would give f2py a shot. The problem is that I have no experience with fortran. I have successfully installed gfortran and f2py on my Linux box and ran the example on thew f2py page, but I have some trouble compiling and running the large program. There are two files, one with a file reader wrapper and one with all the logic. They seem to call each other, but when I compile and link or try f2py, I get errors that they somehow can't find each other: f95 -c FILEWR~1.F f95 -c SMPSREAD.F90 f95 -o smpsread SMPSREAD.o FILEWR~1.o FILEWR~1.o In function `file_wrapper_' FILEWR~1.F(.text+0x3d) undefined reference to `chopen_' usrlibgcci486-linux-gnu4.4.1libgfortranbegin.a(fmain.o) In function `main' (.text+0x27) undefined reference to `MAIN__' collect2 ld returned 1 exit status I also tried changing the name to FILE_WRAPPER.F but that did not help. With f2py I found out I had to include a comment to get it to accept free format, and saved this as a new file and tried: f2py -c -m smpsread smpsread.f90 I get a lot of output and warnings, but the error seems to be this one: getctype: No C-type found in "{'typespec': 'type', 'attrspec': ['allocatable'], 'typename': 'node', 'dimension': [':']}", assuming void. The fortran 90 spms reader can be found here. Any help or suggestions appreciated.

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  • Where can I find BLAS example code (in Fortran)?

    - by Feynman
    I have been searching for decent documentation on blas, and I have found some 315 pages of dense material that ctrl-f does not work on. It provides all the information regarding what input arguments the routines take, but there are a LOT of input arguments and I could really use some example code. I am unable to locate any. I know there has to be some or no one would be able to use these libraries! Specifically, I use ATLAS installed via macports on a mac osx 10.5.8 and I use gfortran from gcc 4.4 (also installed via macports). I am coding in Fortran 90. I am still quite new to Fortran, but I have a fair amount of experience with mathematica, matlab, perl, and shell scripting. I would like to be able to initialize and multiply a dense complex vector by a dense symmetric (but not hermitian) complex matrix. The elements of the matrix are defined through a mathematical function of the indices--call it f(i,j). Could anyone provide some code or a link to some code?

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  • Helping install mrcwa and solve problems with f2py in Ubuntu 14.04 LTS

    - by user288160
    I am sorry if this is the wrong section but I am starting to get desperate, please someone help me... I need to install the program mrcwa-20080820 (sourceforge.net/projects/mrcwa/) because a summer project that I am involved. I need to use it together with anaconda (store.continuum.io/cshop/anaconda/), I already installed Anaconda and apparently it is working. When I type: conda --version I got the expected answer. conda 3.5.2 If I tried to import numpy or scipy with python or simple type f2py there are no errors. So far so good. But when I tried to install this program sudo python setup.py install I got these errors: running install running build sh: 1: f2py: not found cp: cannot stat ‘mrcwaf.so’: No such file or directory running build_py running install_lib running install_egg_info Removing /usr/local/lib/python2.7/dist-packages/mrcwa-20080820.egg-info Writing /usr/local/lib/python2.7/dist-packages/mrcwa-20080820.egg-info Obs: I am trying to use intel fortran 64-bits and Ubuntu 14.04 LTS. So I was checking f2py and tried to execute the program hello world f2py -c -m hello hello.f from here: cens.ioc.ee/projects/f2py2e/index.html#usage and I had some problems too: running build running config_cc unifing config_cc, config, build_clib, build_ext, build commands --compiler options running config_fc unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options running build_src build_src building extension "hello" sources f2py options: [] f2py:> /tmp/tmpf8P4Y3/src.linux-x86_64-2.7/hellomodule.c creating /tmp/tmpf8P4Y3/src.linux-x86_64-2.7 Reading fortran codes... Reading file 'hello.f' (format:fix,strict) Post-processing... Block: hello Block: foo Post-processing (stage 2)... Building modules... Building module "hello"... Constructing wrapper function "foo"... foo(a) Wrote C/API module "hello" to file "/tmp/tmpf8P4Y3/src.linux-x86_64-2.7 /hellomodule.c" adding '/tmp/tmpf8P4Y3/src.linux-x86_64-2.7/fortranobject.c' to sources. adding '/tmp/tmpf8P4Y3/src.linux-x86_64-2.7' to include_dirs. copying /home/felipe/.local/lib/python2.7/site-packages/numpy/f2py/src/fortranobject.c -> /tmp/tmpf8P4Y3/src.linux-x86_64-2.7 copying /home/felipe/.local/lib/python2.7/site-packages/numpy/f2py/src/fortranobject.h -> /tmp/tmpf8P4Y3/src.linux-x86_64-2.7 build_src: building npy-pkg config files running build_ext customize UnixCCompiler customize UnixCCompiler using build_ext customize Gnu95FCompiler Could not locate executable gfortran Could not locate executable f95 customize IntelFCompiler Found executable /opt/intel/composer_xe_2013_sp1.3.174/bin/intel64/ifort customize LaheyFCompiler Could not locate executable lf95 customize PGroupFCompiler Could not locate executable pgfortran customize AbsoftFCompiler Could not locate executable f90 Could not locate executable f77 customize NAGFCompiler customize VastFCompiler customize CompaqFCompiler Could not locate executable fort customize IntelItaniumFCompiler customize IntelEM64TFCompiler customize IntelEM64TFCompiler customize IntelEM64TFCompiler using build_ext building 'hello' extension compiling C sources C compiler: gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC creating /tmp/tmpf8P4Y3/tmp creating /tmp/tmpf8P4Y3/tmp/tmpf8P4Y3 creating /tmp/tmpf8P4Y3/tmp/tmpf8P4Y3/src.linux-x86_64-2.7 compile options: '-I/tmp/tmpf8P4Y3/src.linux-x86_64-2.7 -I/home/felipe/.local/lib/python2.7/site-packages/numpy/core/include -I/home/felipe/anaconda/include/python2.7 -c' gcc: /tmp/tmpf8P4Y3/src.linux-x86_64-2.7/hellomodule.c In file included from /home/felipe/.local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1761:0, from /home/felipe/.local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:17, from /home/felipe/.local/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, from /tmp/tmpf8P4Y3/src.linux-x86_64-2.7/fortranobject.h:13, from /tmp/tmpf8P4Y3/src.linux-x86_64-2.7/hellomodule.c:17: /home/felipe/.local/lib/python2.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it by " \ ^ gcc: /tmp/tmpf8P4Y3/src.linux-x86_64-2.7/fortranobject.c In file included from /home/felipe/.local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1761:0, from /home/felipe/.local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:17, from /home/felipe/.local/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, from /tmp/tmpf8P4Y3/src.linux-x86_64-2.7/fortranobject.h:13, from /tmp/tmpf8P4Y3/src.linux-x86_64-2.7/fortranobject.c:2: /home/felipe/.local/lib/python2.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it by " \ ^ compiling Fortran sources Fortran f77 compiler: /opt/intel/composer_xe_2013_sp1.3.174/bin/intel64/ifort -FI -fPIC -xhost -openmp -fp-model strict Fortran f90 compiler: /opt/intel/composer_xe_2013_sp1.3.174/bin/intel64/ifort -FR -fPIC -xhost -openmp -fp-model strict Fortran fix compiler: /opt/intel/composer_xe_2013_sp1.3.174/bin/intel64/ifort -FI -fPIC -xhost -openmp -fp-model strict compile options: '-I/tmp/tmpf8P4Y3/src.linux-x86_64-2.7 -I/home/felipe/.local /lib/python2.7/site-packages/numpy/core/include -I/home/felipe/anaconda/include/python2.7 -c' ifort:f77: hello.f /opt/intel/composer_xe_2013_sp1.3.174/bin/intel64/ifort -shared -shared -nofor_main /tmp/tmpf8P4Y3/tmp/tmpf8P4Y3/src.linux-x86_64-2.7/hellomodule.o /tmp/tmpf8P4Y3 /tmp/tmpf8P4Y3/src.linux-x86_64-2.7/fortranobject.o /tmp/tmpf8P4Y3/hello.o -L/home/felipe /anaconda/lib -lpython2.7 -o ./hello.so Removing build directory /tmp/tmpf8P4Y3 Please help me I am new in ubuntu and python. I really need this program, my advisor is waiting an answer. Thank you very much, Felipe Oliveira.

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  • Mac 10.6 Universal Binary scipy: cephes/specfun "_aswfa_" symbol not found

    - by Markus
    Hi folks, I can't get scipy to function in 32 bit mode when compiled as a i386/x86_64 universal binary, and executed on my 64 bit 10.6.2 MacPro1,1. My python setup With the help of this answer, I built a 32/64 bit intel universal binary of python 2.6.4 with the intention of using the arch command to select between the architectures. (I managed to make some universal binaries of a few libraries I wanted using lipo.) That all works. I then installed scipy according to the instructions on hyperjeff's article, only with more up-to-date numpy (1.4.0) and skipping the bit about moving numpy aside briefly during the installation of scipy. Now, everything except scipy seems to be working as far as I can tell, and I can indeed select between 32 and 64 bit mode using arch -i386 python and arch -x86_64 python. The error Scipy complains in 32 bit mode: $ arch -x86_64 python -c "import scipy.interpolate; print 'success'" success $ arch -i386 python -c "import scipy.interpolate; print 'success'" Traceback (most recent call last): File "<string>", line 1, in <module> File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy/interpolate/__init__.py", line 7, in <module> from interpolate import * File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy/interpolate/interpolate.py", line 13, in <module> import scipy.special as spec File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy/special/__init__.py", line 8, in <module> from basic import * File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy/special/basic.py", line 8, in <module> from _cephes import * ImportError: dlopen(/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy/special/_cephes.so, 2): Symbol not found: _aswfa_ Referenced from: /Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy/special/_cephes.so Expected in: flat namespace in /Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy/special/_cephes.so Attempt at tracking down the problem It looks like scipy.interpolate imports something called _cephes, which looks for a symbol called _aswfa_ but can't find it in 32 bit mode. Browsing through scipy's source, I find an ASWFA subroutine in specfun.f. The only scipy product file with a similar name is specfun.so, but both that and _cephes.so appear to be universal binaries: $ cd /Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy/special/ $ file _cephes.so specfun.so _cephes.so: Mach-O universal binary with 2 architectures _cephes.so (for architecture i386): Mach-O bundle i386 _cephes.so (for architecture x86_64): Mach-O 64-bit bundle x86_64 specfun.so: Mach-O universal binary with 2 architectures specfun.so (for architecture i386): Mach-O bundle i386 specfun.so (for architecture x86_64): Mach-O 64-bit bundle x86_64 Ho hum. I'm stuck. Things I may try but haven't figured out how yet include compiling specfun.so myself manually, somehow. I would imagine that scipy isn't broken for all 32 bit machines, so I guess something is wrong with the way I've installed it, but I can't figure out what. I don't really expect a full answer given my fairly unique (?) setup, but if anyone has any clues that might point me in the right direction, they'd be greatly appreciated. (edit) More details to address questions: I'm using gfortran (GNU Fortran from GCC 4.2.1 Apple Inc. build 5646). Python 2.6.4 was installed more-or-less like so: cd /tmp curl -O http://www.python.org/ftp/python/2.6.4/Python-2.6.4.tar.bz2 tar xf Python-2.6.4.tar.bz2 cd Python-2.6.4 # Now replace buggy pythonw.c file with one that supports the "arch" command: curl http://bugs.python.org/file14949/pythonw.c | sed s/2.7/2.6/ > Mac/Tools/pythonw.c ./configure --enable-framework=/Library/Frameworks --enable-universalsdk=/ --with-universal-archs=intel make -j4 sudo make frameworkinstall Scipy 0.7.1 was installed pretty much as described as here, but it boils down to a simple sudo python setup.py install. It would indeed appear that the symbol is undefined in the i386 architecture if you look at the _cephes library with nm, as suggested by David Cournapeau: $ nm -arch x86_64 /Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy/special/_cephes.so | grep _aswfa_ 00000000000d4950 T _aswfa_ 000000000011e4b0 d _oblate_aswfa_data 000000000011e510 d _oblate_aswfa_nocv_data (snip) $ nm -arch i386 /Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy/special/_cephes.so | grep _aswfa_ U _aswfa_ 0002e96c d _oblate_aswfa_data 0002e99c d _oblate_aswfa_nocv_data (snip) however, I can't yet explain its absence.

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  • Recompiling an old fortran 2/4\66 program that was compiled for os\2 need it to run in dos

    - by Mike Hansen
    I am helping an old scientist with some problems and have 1 program that he found and modified about 20 yrs. ago, and runs fine as a 32 bit os\2 executable but i need it to run under dos! I am not a programmer but a good hardware & software man, so I'am pretty stupid about this problem, but here go's I have downloaded 6 different compilers watcom77,silverfrost ftn95,gfortran,2 versions of g77 and f80. Watcom says it is to old of program,find older compiler,silverfrost opens it,debugs, etc. but is changing all the subroutines from "real" to "complex" and vice-vesa,and the g77's seem to install perfectly (library links and etc.) but wont even compile the test.f programs.My problem is 1; to recompile "as is" or "upgrade" the code? PROGRAM xconvlv INTEGER N,N2,M PARAMETER (N=2048,N2=2048,M=128) INTEGER i,isign REAL data(n),respns(m),resp(n),ans(n2),t3(n),DUMMY OPEN(UNIT=1, FILE='C:\QKBAS20\FDATA1.DAT') DO 1 i=1,N READ(1,*) T3(i), data(i), DUMMY continue CLOSE(UNIT-1) do 12 i=1,N respns(i)=data(i) resp(i)=respns(i) continue isign=-1 call convlv(data,N,resp,M,isign,ans) OPEN(UNIT=1,FILE='C:\QKBAS20\FDATA9.DAT') DO 14 i=1,N WRITE(1,*) T3(i), ans(i) continue END SUBROUTINE CONVLV(data,n,respns,m,isign,ans) INTEGER isign,m,n,NMAX REAL data(n),respns(n) COMPLEX ans(n) PARAMETER (NMAX=4096) * uses realft, twofft INTEGER i,no2 COMPLEX fft (NMAX) do 11 i=1, (m-1)/2 respns(n+1-i)=respns(m+1-i) continue do 12 i=(m+3)/2,n-(m-1)/2 respns(i)=0.0 continue call twofft (data,respns,fft,ans,n) no2=n/2 do 13 i=1,no2+1 if (isign.eq.1) then ans(i)=fft(i)*ans(i)/no2 else if (isign.eq.-1) then if (abs(ans(i)) .eq.0.0) pause ans(i)=fft(i)/ans(i)/no2 else pause 'no meaning for isign in convlv' endif continue ans(1)=cmplx(real (ans(1)),real (ans(no2+1))) call realft(ans,n,-1) return END SUBROUTINE realft(data,n,isign) INTEGER isign,n REAL data(n) * uses four1 INTEGER i,i1,i2,i3,i4,n2p3 REAL c1,c2,hli,hir,h2i,h2r,wis,wrs DOUBLE PRECISION theta,wi,wpi,wpr,wr,wtemp theta=3.141592653589793d0/dble(n/2) cl=0.5 if (isign.eq.1) then c2=-0.5 call four1(data,n/2,+1) else c2=0.5 theta=-theta endif (etc.,etc., etc.) SUBROUTINE twofft(data,data2,fft1,fft2,n) INTEGER n REAL data1(n,data2(n) COMPLEX fft1(n), fft2(n) * uses four1 INTEGER j,n2 COMPLEX h1,h2,c1,c2 c1=cmplx(0.5,0.0) c2=cmplx(0.0,-0.5) do 11 j=1,n fft1(j)=cmplx(data1(j),data2(j) continue call four1 (fft1,n,1) fft2(1)=cmplx(aimag(fft1(1)),0.0) fft1(1)=cmplx(real(fft1(1)),0.0) n2=n+2 do 12 j=2,n/2+1 h1=c1*(fft1(j)+conjg(fft1(n2-j))) h2=c2*(fft1(j)-conjg(fft1(n2-j))) fft1(j)=h1 fft1(n2-j)=conjg(h1) fft2(j)=h2 fft2(n2-j)=conjg(h2) continue return END SUBROUTINE four1(data,nn,isign) INTEGER isign,nn REAL data(2*nn) INTEGER i,istep,j,m,mmax,n REAL tempi,tempr DOUBLE PRECISION theta, wi,wpi,wpr,wr,wtemp n=2*nn j=1 do 11 i=1,n,2 if(j.gt.i)then tempr=data(j) tempi=data(j+1) (etc.,etc.,etc.,) continue mmax=istep goto 2 endif return END There are 4 subroutines with this that are about 3 pages of code and whould be much easier to e-mail to someone if their able to help me with this.My e-mail is [email protected] , or if someone could tell me where to get a "working" compiler that could recompile this? THANK-YOU, THANK-YOU,and THANK-YOU for any help with this! The errors Iam getting are; 1.In a call to CONVLV from another procedure,the first argument was of a type REAL(kind=1), it is now a COMPLEX(kind=1) 2.In a call to REALFT from another procedure, ... COMPLEX(kind=1) it is now a REAL(kind=1) 3.In a call to TWOFFT from...COMPLEX(kind-1) it is now a REAL(kind=1) 4.In a previous call to FOUR1, the first argument was of a type REAL(kind=1) it is now a COMPLEX(kind=1).

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  • Error compiling GLib in Ubuntu 14.04 (trying to install GimpShop)

    - by Nicolás Salvarrey
    I'm kinda new in Linux, so please take it easy on the most complicated stuff. I'm trying to install GimpShop. Installation guide asks me to install GLib first, and when I try to compile it using the make command I get errors. When I run the ./configure --prefix=/usr command, I get this: checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether to enable maintainer-specific portions of Makefiles... no checking build system type... x86_64-unknown-linux-gnu checking host system type... x86_64-unknown-linux-gnu checking for the BeOS... no checking for Win32... no checking whether to enable garbage collector friendliness... no checking whether to disable memory pools... no checking for gcc... gcc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ANSI C... none needed checking for style of include used by make... GNU checking dependency style of gcc... gcc3 checking for c++... no checking for g++... no checking for gcc... gcc checking whether we are using the GNU C++ compiler... no checking whether gcc accepts -g... no checking dependency style of gcc... gcc3 checking for gcc option to accept ANSI C... none needed checking for a BSD-compatible install... /usr/bin/install -c checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking for _LARGE_FILES value needed for large files... no checking for pkg-config... /usr/bin/pkg-config checking for gawk... (cached) mawk checking for perl5... no checking for perl... perl checking for indent... no checking for perl... /usr/bin/perl checking for iconv_open... yes checking how to run the C preprocessor... gcc -E checking for egrep... grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking locale.h usability... yes checking locale.h presence... yes checking for locale.h... yes checking for LC_MESSAGES... yes checking libintl.h usability... yes checking libintl.h presence... yes checking for libintl.h... yes checking for ngettext in libc... yes checking for dgettext in libc... yes checking for bind_textdomain_codeset... yes checking for msgfmt... /usr/bin/msgfmt checking for dcgettext... yes checking for gmsgfmt... /usr/bin/msgfmt checking for xgettext... /usr/bin/xgettext checking for catalogs to be installed... am ar az be bg bn bs ca cs cy da de el en_CA en_GB eo es et eu fa fi fr ga gl gu he hi hr id is it ja ko lt lv mk mn ms nb ne nl nn no or pa pl pt pt_BR ro ru sk sl sq sr sr@ije sr@Latn sv ta tl tr uk vi wa xh yi zh_CN zh_TW checking for a sed that does not truncate output... /bin/sed checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for /usr/bin/ld option to reload object files... -r checking for BSD-compatible nm... /usr/bin/nm -B checking whether ln -s works... yes checking how to recognise dependent libraries... pass_all checking dlfcn.h usability... yes checking dlfcn.h presence... yes checking for dlfcn.h... yes checking for g77... no checking for f77... no checking for xlf... no checking for frt... no checking for pgf77... no checking for fort77... no checking for fl32... no checking for af77... no checking for f90... no checking for xlf90... no checking for pgf90... no checking for epcf90... no checking for f95... no checking for fort... no checking for xlf95... no checking for ifc... no checking for efc... no checking for pgf95... no checking for lf95... no checking for gfortran... no checking whether we are using the GNU Fortran 77 compiler... no checking whether accepts -g... no checking the maximum length of command line arguments... 32768 checking command to parse /usr/bin/nm -B output from gcc object... ok checking for objdir... .libs checking for ar... ar checking for ranlib... ranlib checking for strip... strip checking if gcc static flag works... yes checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC checking if gcc PIC flag -fPIC works... yes checking if gcc supports -c -o file.o... yes checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... no configure: creating libtool appending configuration tag "CXX" to libtool appending configuration tag "F77" to libtool checking for extra flags to get ANSI library prototypes... none needed checking for extra flags for POSIX compliance... none needed checking for ANSI C header files... (cached) yes checking for vprintf... yes checking for _doprnt... no checking for working alloca.h... yes checking for alloca... yes checking for atexit... yes checking for on_exit... yes checking for char... yes checking size of char... 1 checking for short... yes checking size of short... 2 checking for long... yes checking size of long... 8 checking for int... yes checking size of int... 4 checking for void *... yes checking size of void *... 8 checking for long long... yes checking size of long long... 8 checking for __int64... no checking size of __int64... 0 checking for format to printf and scanf a guint64... %llu checking for an ANSI C-conforming const... yes checking if malloc() and friends prototypes are gmem.h compatible... no checking for growing stack pointer... yes checking for __inline... yes checking for __inline__... yes checking for inline... yes checking if inline functions in headers work... yes checking for ISO C99 varargs macros in C... yes checking for ISO C99 varargs macros in C++... no checking for GNUC varargs macros... yes checking for GNUC visibility attribute... yes checking whether byte ordering is bigendian... no checking dirent.h usability... yes checking dirent.h presence... yes checking for dirent.h... yes checking float.h usability... yes checking float.h presence... yes checking for float.h... yes checking limits.h usability... yes checking limits.h presence... yes checking for limits.h... yes checking pwd.h usability... yes checking pwd.h presence... yes checking for pwd.h... yes checking sys/param.h usability... yes checking sys/param.h presence... yes checking for sys/param.h... yes checking sys/poll.h usability... yes checking sys/poll.h presence... yes checking for sys/poll.h... yes checking sys/select.h usability... yes checking sys/select.h presence... yes checking for sys/select.h... yes checking for sys/types.h... (cached) yes checking sys/time.h usability... yes checking sys/time.h presence... yes checking for sys/time.h... yes checking sys/times.h usability... yes checking sys/times.h presence... yes checking for sys/times.h... yes checking for unistd.h... (cached) yes checking values.h usability... yes checking values.h presence... yes checking for values.h... yes checking for stdint.h... (cached) yes checking sched.h usability... yes checking sched.h presence... yes checking for sched.h... yes checking langinfo.h usability... yes checking langinfo.h presence... yes checking for langinfo.h... yes checking for nl_langinfo... yes checking for nl_langinfo and CODESET... yes checking whether we are using the GNU C Library 2.1 or newer... yes checking stddef.h usability... yes checking stddef.h presence... yes checking for stddef.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for setlocale... yes checking for size_t... yes checking size of size_t... 8 checking for the appropriate definition for size_t... unsigned long checking for lstat... yes checking for strerror... yes checking for strsignal... yes checking for memmove... yes checking for mkstemp... yes checking for vsnprintf... yes checking for stpcpy... yes checking for strcasecmp... yes checking for strncasecmp... yes checking for poll... yes checking for getcwd... yes checking for nanosleep... yes checking for vasprintf... yes checking for setenv... yes checking for unsetenv... yes checking for getc_unlocked... yes checking for readlink... yes checking for symlink... yes checking for C99 vsnprintf... yes checking whether printf supports positional parameters... yes checking for signed... yes checking for long long... (cached) yes checking for long double... yes checking for wchar_t... yes checking for wint_t... yes checking for size_t... (cached) yes checking for ptrdiff_t... yes checking for inttypes.h... yes checking for stdint.h... yes checking for snprintf... yes checking for C99 snprintf... yes checking for sys_errlist... yes checking for sys_siglist... yes checking for sys_siglist declaration... yes checking for fd_set... yes, found in sys/types.h checking whether realloc (NULL,) will work... yes checking for nl_langinfo (CODESET)... yes checking for OpenBSD strlcpy/strlcat... no checking for an implementation of va_copy()... yes checking for an implementation of __va_copy()... yes checking whether va_lists can be copied by value... no checking for dlopen... no checking for NSLinkModule... no checking for dlopen in -ldl... yes checking for dlsym in -ldl... yes checking for RTLD_GLOBAL brokenness... no checking for preceeding underscore in symbols... no checking for dlerror... yes checking for the suffix of shared libraries... .so checking for gspawn implementation... gspawn.lo checking for GIOChannel implementation... giounix.lo checking for platform-dependent source... checking whether to compile timeloop... yes checking if building for some Win32 platform... no checking for thread implementation... posix checking thread related cflags... -pthread checking for sched_get_priority_min... yes checking thread related libraries... -pthread checking for localtime_r... yes checking for posix getpwuid_r... yes checking size of pthread_t... 8 checking for pthread_attr_setstacksize... yes checking for minimal/maximal thread priority... sched_get_priority_min(SCHED_OTHER)/sched_get_priority_max(SCHED_OTHER) checking for pthread_setschedparam... yes checking for posix yield function... sched_yield checking size of pthread_mutex_t... 40 checking byte contents of PTHREAD_MUTEX_INITIALIZER... 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 checking whether to use assembler code for atomic operations... x86_64 checking value of POLLIN... 1 checking value of POLLOUT... 4 checking value of POLLPRI... 2 checking value of POLLERR... 8 checking value of POLLHUP... 16 checking value of POLLNVAL... 32 checking for EILSEQ... yes configure: creating ./config.status config.status: creating glib-2.0.pc config.status: creating glib-2.0-uninstalled.pc config.status: creating gmodule-2.0.pc config.status: creating gmodule-no-export-2.0.pc config.status: creating gmodule-2.0-uninstalled.pc config.status: creating gthread-2.0.pc config.status: creating gthread-2.0-uninstalled.pc config.status: creating gobject-2.0.pc config.status: creating gobject-2.0-uninstalled.pc config.status: creating glib-zip config.status: creating glib-gettextize config.status: creating Makefile config.status: creating build/Makefile config.status: creating build/win32/Makefile config.status: creating build/win32/dirent/Makefile config.status: creating glib/Makefile config.status: creating glib/libcharset/Makefile config.status: creating glib/gnulib/Makefile config.status: creating gmodule/Makefile config.status: creating gmodule/gmoduleconf.h config.status: creating gobject/Makefile config.status: creating gobject/glib-mkenums config.status: creating gthread/Makefile config.status: creating po/Makefile.in config.status: creating docs/Makefile config.status: creating docs/reference/Makefile config.status: creating docs/reference/glib/Makefile config.status: creating docs/reference/glib/version.xml config.status: creating docs/reference/gobject/Makefile config.status: creating docs/reference/gobject/version.xml config.status: creating tests/Makefile config.status: creating tests/gobject/Makefile config.status: creating m4macros/Makefile config.status: creating config.h config.status: config.h is unchanged config.status: executing depfiles commands config.status: executing default-1 commands config.status: executing glibconfig.h commands config.status: glibconfig.h is unchanged config.status: executing chmod-scripts commands nsalvarrey@Delleuze:~/glib-2.6.3$ ^C nsalvarrey@Delleuze:~/glib-2.6.3$ And then, with the make command, I get this: galias.h:83:39: error: 'g_ascii_digit_value' aliased to undefined symbol 'IA__g_ascii_digit_value' extern __typeof (g_ascii_digit_value) g_ascii_digit_value __attribute((alias("IA__g_ascii_digit_value"), visibility("default"))); ^ In file included from garray.c:35:0: galias.h:31:35: error: 'g_allocator_new' aliased to undefined symbol 'IA__g_allocator_new' extern __typeof (g_allocator_new) g_allocator_new __attribute((alias("IA__g_allocator_new"), visibility("default"))); ^ make[4]: *** [garray.lo] Error 1 make[4]: se sale del directorio «/home/nsalvarrey/glib-2.6.3/glib» make[3]: *** [all-recursive] Error 1 make[3]: se sale del directorio «/home/nsalvarrey/glib-2.6.3/glib» make[2]: *** [all] Error 2 make[2]: se sale del directorio «/home/nsalvarrey/glib-2.6.3/glib» make[1]: *** [all-recursive] Error 1 make[1]: se sale del directorio «/home/nsalvarrey/glib-2.6.3» make: *** [all] Error 2 nsalvarrey@Delleuze:~/glib-2.6.3$ (it's actually a lot longer) Can somebody help me?

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  • Why do I get "unsupported architecture" errors trying to install a Python library in OSX?

    - by Emma518
    I am trying to install a Python library in the Presto package, source http://www.cv.nrao.edu/~sransom/presto/ Using 'gmake fftfit' I get the following error: cd fftfit_src ; f2py-2.7 -c fftfit.pyf *.f running build running config_cc unifing config_cc, config, build_clib, build_ext, build commands --compiler options running config_fc unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options running build_src build_src building extension "fftfit" sources creating /var/folders/sx/j_l_qvys4bv00_38pfvy3m8h0000gp/T/tmp9MmLz8/src.macosx-10.9-x86_64-2.7 f2py options: [] f2py: fftfit.pyf Reading fortran codes... Reading file 'fftfit.pyf' (format:free) Post-processing... Block: fftfit Block: cprof Block: fftfit Post-processing (stage 2)... Building modules... Building module "fftfit"... Constructing wrapper function "cprof"... c,amp,pha = cprof(y,[nmax,nh]) Constructing wrapper function "fftfit"... shift,eshift,snr,esnr,b,errb,ngood = fftfit(prof,s,phi,[nmax]) Wrote C/API module "fftfit" to file "/var/folders/sx/j_l_qvys4bv00_38pfvy3m8h0000gp/T/tmp9MmLz8/src.macosx-10.9-x86_64- 2.7/fftfitmodule.c" adding '/var/folders/sx/j_l_qvys4bv00_38pfvy3m8h0000gp/T/tmp9MmLz8/src.macosx-10.9-x86_64-2.7/fortranobject.c' to sources. adding '/var/folders/sx/j_l_qvys4bv00_38pfvy3m8h0000gp/T/tmp9MmLz8/src.macosx-10.9-x86_64-2.7' to include_dirs. copying /Library/Python/2.7/site-packages/numpy-1.8.2-py2.7-macosx-10.9- intel.egg/numpy/f2py/src/fortranobject.c -> /var/folders/sx/j_l_qvys4bv00_38pfvy3m8h0000gp/T/tmp9MmLz8/src.macosx-10.9-x86_64-2.7 copying /Library/Python/2.7/site-packages/numpy-1.8.2-py2.7-macosx-10.9-intel.egg/numpy/f2py/src/fortranobject.h -> /var/folders/sx/j_l_qvys4bv00_38pfvy3m8h0000gp/T/tmp9MmLz8/src.macosx-10.9-x86_64-2.7 build_src: building npy-pkg config files running build_ext customize UnixCCompiler customize UnixCCompiler using build_ext customize Gnu95FCompiler Found executable /usr/local/bin/gfortran customize Gnu95FCompiler customize Gnu95FCompiler using build_ext building 'fftfit' extension compiling C sources C compiler: /usr/bin/clang -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -arch ppc -arch i386 -arch x86_64 -g -O2 creating /var/folders/sx/j_l_qvys4bv00_38pfvy3m8h0000gp/T/tmp9MmLz8/var creating /var/folders/sx/j_l_qvys4bv00_38pfvy3m8h0000gp/T/tmp9MmLz8/var/folders creating /var/folders/sx/j_l_qvys4bv00_38pfvy3m8h0000gp/T/tmp9MmLz8/var/folders/sx creating /var/folders/sx/j_l_qvys4bv00_38pfvy3m8h0000gp/T/tmp9MmLz8/var/folders/sx/j_l_qvys4bv00_38pfvy3m8h0000gp creating /var/folders/sx/j_l_qvys4bv00_38pfvy3m8h0000gp/T/tmp9MmLz8/var/folders/sx/j_l_qvys4bv00_38pfvy3m8h00 00gp/T creating /var/folders/sx/j_l_qvys4bv00_38pfvy3m8h0000gp/T/tmp9MmLz8/var/folders/sx/j_l_qvys4bv00_38pfvy3m8h00 00gp/T/tmp9MmLz8 creating /var/folders/sx/j_l_qvys4bv00_38pfvy3m8h0000gp/T/tmp9MmLz8/var/folders/sx/j_l_qvys4bv00_38pfvy3m8h00 00gp/T/tmp9MmLz8/src.macosx-10.9-x86_64-2.7 compile options: '-I/var/folders/sx/j_l_qvys4bv00_38pfvy3m8h0000gp/T/tmp9MmLz8/src.macosx-10.9- x86_64-2.7 -I/Library/Python/2.7/site-packages/numpy-1.8.2-py2.7-macosx-10.9- intel.egg/numpy/core/include - I/opt/local/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c' clang: /var/folders/sx/j_l_qvys4bv00_38pfvy3m8h0000gp/T/tmp9MmLz8/src.macosx-10.9-x86_64- 2.7/fftfitmodule.c In file included from /var/folders/sx/j_l_qvys4bv00_38pfvy3m8h0000gp/T/tmp9MmLz8/src.macosx- 10.9-x86_64-2.7/fftfitmodule.c:16: In file included from /opt/local/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7/Python.h:19: In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/ 5.1/include/limits.h:38: In file included from /usr/include/limits.h:63: /usr/include/sys/cdefs.h:658:2: error: Unsupported architecture #error Unsupported architecture ^ In file included from /var/folders/sx/j_l_qvys4bv00_38pfvy3m8h0000gp/T/tmp9MmLz8/src.macosx- 10.9-x86_64-2.7/fftfitmodule.c:16: In file included from /opt/local/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7/Python.h:19: In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/ 5.1/include/limits.h:38: In file included from /usr/include/limits.h:64: /usr/include/machine/limits.h:8:2: error: architecture not supported #error architecture not supported ^ In file included from /var/folders/sx/j_l_qvys4bv00_38pfvy3m8h0000gp/T/tmp9MmLz8/src.macosx- 10.9-x86_64-2.7/fftfitmodule.c:16: In file included from /opt/local/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7/Python.h:33: In file included from /usr/include/stdio.h:67: In file included from /usr/include/_types.h:27: In file included from /usr/include/sys/_types.h:33: /usr/include/machine/_types.h:34:2: error: architecture not supported #error architecture not supported ^ In file included from /var/folders/sx/j_l_qvys4bv00_38pfvy3m8h0000gp/T/tmp9MmLz8/src.macosx- 10.9-x86_64-2.7/fftfitmodule.c:16: In file included from /opt/local/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7/Python.h:33: In file included from /usr/include/stdio.h:67: In file included from /usr/include/_types.h:27: /usr/include/sys/_types.h:94:9: error: unknown type name '__int64_t' typedef __int64_t __darwin_blkcnt_t; /* total blocks */ ^ /usr/include/sys/_types.h:95:9: error: unknown type name '__int32_t' typedef __int32_t __darwin_blksize_t; /* preferred block size */ ^ /usr/include/sys/_types.h:96:9: error: unknown type name '__int32_t' typedef __int32_t __darwin_dev_t; /* dev_t */ ^ /usr/include/sys/_types.h:99:9: error: unknown type name '__uint32_t' typedef __uint32_t __darwin_gid_t; /* [???] process and group IDs */ ^ /usr/include/sys/_types.h:100:9: error: unknown type name '__uint32_t' typedef __uint32_t __darwin_id_t; /* [XSI] pid_t, uid_t, or gid_t*/ ^ /usr/include/sys/_types.h:101:9: error: unknown type name '__uint64_t' typedef __uint64_t __darwin_ino64_t; /* [???] Used for 64 bit inodes */ ^ /usr/include/sys/_types.h:107:9: error: unknown type name '__darwin_natural_t' typedef __darwin_natural_t __darwin_mach_port_name_t; /* Used by mach */ ^ /usr/include/sys/_types.h:109:9: error: unknown type name '__uint16_t' typedef __uint16_t __darwin_mode_t; /* [???] Some file attributes */ ^ /usr/include/sys/_types.h:110:9: error: unknown type name '__int64_t' typedef __int64_t __darwin_off_t; /* [???] Used for file sizes */ ^ /usr/include/sys/_types.h:111:9: error: unknown type name '__int32_t' typedef __int32_t __darwin_pid_t; /* [???] process and group IDs */ ^ /usr/include/sys/_types.h:131:9: error: unknown type name '__uint32_t' typedef __uint32_t __darwin_sigset_t; /* [???] signal set */ ^ /usr/include/sys/_types.h:132:9: error: unknown type name '__int32_t' typedef __int32_t __darwin_suseconds_t; /* [???] microseconds */ ^ /usr/include/sys/_types.h:133:9: error: unknown type name '__uint32_t' typedef __uint32_t __darwin_uid_t; /* [???] user IDs */ ^ /usr/include/sys/_types.h:134:9: error: unknown type name '__uint32_t' typedef __uint32_t __darwin_useconds_t; /* [???] microseconds */ ^ In file included from /var/folders/sx/j_l_qvys4bv00_38pfvy3m8h0000gp/T/tmp9MmLz8/src.macosx- 10.9-x86_64-2.7/fftfitmodule.c:16: In file included from /opt/local/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7/Python.h:33: In file included from /usr/include/stdio.h:71: /usr/include/sys/_types/_va_list.h:31:9: error: unknown type name '__darwin_va_list'; did you mean '__builtin_va_list'? typedef __darwin_va_list va_list; ^ note: '__builtin_va_list' declared here In file included from /var/folders/sx/j_l_qvys4bv00_38pfvy3m8h0000gp/T/tmp9MmLz8/src.macosx- 10.9-x86_64-2.7/fftfitmodule.c:16: In file included from /opt/local/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7/Python.h:33: In file included from /usr/include/stdio.h:72: /usr/include/sys/_types/_size_t.h:30:9: error: unknown type name '__darwin_size_t'; did you mean '__darwin_ino_t'? typedef __darwin_size_t size_t; ^ /usr/include/sys/_types.h:103:26: note: '__darwin_ino_t' declared here typedef __darwin_ino64_t __darwin_ino_t; /* [???] Used for inodes */ ^ fatal error: too many errors emitted, stopping now [-ferror-limit=] 20 errors generated. In file included from /var/folders/sx/j_l_qvys4bv00_38pfvy3m8h0000gp/T/tmp9MmLz8/src.macosx- 10.9-x86_64-2.7/fftfitmodule.c:16: In file included from /opt/local/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7/Python.h:19: In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/5.1/include/limits.h:38: In file included from /usr/include/limits.h:63: /usr/include/sys/cdefs.h:658:2: error: Unsupported architecture #error Unsupported architecture ^ In file included from /var/folders/sx/j_l_qvys4bv00_38pfvy3m8h0000gp/T/tmp9MmLz8/src.macosx- 10.9-x86_64-2.7/fftfitmodule.c:16: In file included from /opt/local/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7/Python.h:19: In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/ 5.1/include/limits.h:38: In file included from /usr/include/limits.h:64: /usr/include/machine/limits.h:8:2: error: architecture not supported #error architecture not supported ^ In file included from /var/folders/sx/j_l_qvys4bv00_38pfvy3m8h0000gp/T/tmp9MmLz8/src.macosx- 10.9-x86_64-2.7/fftfitmodule.c:16: In file included from /opt/local/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7/Python.h:33: In file included from /usr/include/stdio.h:67: In file included from /usr/include/_types.h:27: In file included from /usr/include/sys/_types.h:33: /usr/include/machine/_types.h:34:2: error: architecture not supported #error architecture not supported ^ In file included from /var/folders/sx/j_l_qvys4bv00_38pfvy3m8h0000gp/T/tmp9MmLz8/src.macosx- 10.9-x86_64-2.7/fftfitmodule.c:16: In file included from /opt/local/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7/Python.h:33: In file included from /usr/include/stdio.h:67: In file included from /usr/include/_types.h:27: /usr/include/sys/_types.h:94:9: error: unknown type name '__int64_t' typedef __int64_t __darwin_blkcnt_t; /* total blocks */ ^ /usr/include/sys/_types.h:95:9: error: unknown type name '__int32_t' typedef __int32_t __darwin_blksize_t; /* preferred block size */ ^ /usr/include/sys/_types.h:96:9: error: unknown type name '__int32_t' typedef __int32_t __darwin_dev_t; /* dev_t */ ^ /usr/include/sys/_types.h:99:9: error: unknown type name '__uint32_t' typedef __uint32_t __darwin_gid_t; /* [???] process and group IDs */ ^ /usr/include/sys/_types.h:100:9: error: unknown type name '__uint32_t' typedef __uint32_t __darwin_id_t; /* [XSI] pid_t, uid_t, or gid_t*/ ^ /usr/include/sys/_types.h:101:9: error: unknown type name '__uint64_t' typedef __uint64_t __darwin_ino64_t; /* [???] Used for 64 bit inodes */ ^ /usr/include/sys/_types.h:107:9: error: unknown type name '__darwin_natural_t' typedef __darwin_natural_t __darwin_mach_port_name_t; /* Used by mach */ ^ /usr/include/sys/_types.h:109:9: error: unknown type name '__uint16_t' typedef __uint16_t __darwin_mode_t; /* [???] Some file attributes */ ^ /usr/include/sys/_types.h:110:9: error: unknown type name '__int64_t' typedef __int64_t __darwin_off_t; /* [???] Used for file sizes */ ^ /usr/include/sys/_types.h:111:9: error: unknown type name '__int32_t' typedef __int32_t __darwin_pid_t; /* [???] process and group IDs */ ^ /usr/include/sys/_types.h:131:9: error: unknown type name '__uint32_t' typedef __uint32_t __darwin_sigset_t; /* [???] signal set */ ^ /usr/include/sys/_types.h:132:9: error: unknown type name '__int32_t' typedef __int32_t __darwin_suseconds_t; /* [???] microseconds */ ^ /usr/include/sys/_types.h:133:9: error: unknown type name '__uint32_t' typedef __uint32_t __darwin_uid_t; /* [???] user IDs */ ^ /usr/include/sys/_types.h:134:9: error: unknown type name '__uint32_t' typedef __uint32_t __darwin_useconds_t; /* [???] microseconds */ ^ In file included from /var/folders/sx/j_l_qvys4bv00_38pfvy3m8h0000gp/T/tmp9MmLz8/src.macosx-10.9-x86_64-2.7/fftfitmodule.c:16: In file included from /opt/local/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7/Python.h:33: In file included from /usr/include/stdio.h:71: /usr/include/sys/_types/_va_list.h:31:9: error: unknown type name '__darwin_va_list'; did you mean '__builtin_va_list'? typedef __darwin_va_list va_list; ^ note: '__builtin_va_list' declared here In file included from /var/folders/sx/j_l_qvys4bv00_38pfvy3m8h0000gp/T/tmp9MmLz8/src.macosx-10.9-x86_64-2.7/fftfitmodule.c:16: In file included from /opt/local/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7/Python.h:33: In file included from /usr/include/stdio.h:72: /usr/include/sys/_types/_size_t.h:30:9: error: unknown type name '__darwin_size_t'; did you mean '__darwin_ino_t'? typedef __darwin_size_t size_t; ^ /usr/include/sys/_types.h:103:26: note: '__darwin_ino_t' declared here typedef __darwin_ino64_t __darwin_ino_t; /* [???] Used for inodes */ ^ fatal error: too many errors emitted, stopping now [-ferror-limit=] 20 errors generated. error: Command "/usr/bin/clang -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -arch ppc -arch i386 -arch x86_64 -g -O2 -I/var/folders/sx/j_l_qvys4bv00_38pfvy3m8h0000gp/T/tmp9MmLz8/src.macosx- 10.9-x86_64-2.7 -I/Library/Python/2.7/site-packages/numpy-1.8.2-py2.7-macosx-10.9- intel.egg/numpy/core/include - I/opt/local/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c /var/folders/sx/j_l_qvys4bv00_38pfvy3m8h0000gp/T/tmp9MmLz8/src.macosx-10.9-x86_64-2.7/fftfitmodule.c -o /var/folders/sx/j_l_qvys4bv00_38pfvy3m8h0000gp/T/tmp9MmLz8/var/folders/sx/j_l_qvys4bv00_38pfvy3m8h00 00gp/T/tmp9MmLz8/src.macosx-10.9-x86_64-2.7/fftfitmodule.o" failed with exit status 1 Makefile:5: recipe for target 'fftfit' failed gmake: *** [fftfit] Error 1 How can I solve this architecture problem?

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