Hi,

I'm trying to install numpy on a system where I not have root access and have my own installation of python installed in ~/bin/ (strange location, but too many scripts point here to change it now). I have the custom installation because the system I'm working on has a really old version of python (2.3). Anyway, I have lapack and ATLAS properly compiled from source and point to them in my site.cfg, but I get an error message when I try to build. Output from setup.py is as follows.

Running from numpy source directory. F2PY Version 2 blasoptinfo: blasmklinfo: libraries mkl,vml,guide not found in /hosts/nas1/shares/maxa/home/mzhou/bin/lib NOT AVAILABLE

atlasblasthreadsinfo: Setting PTATLAS=ATLAS Setting PTATLAS=ATLAS Setting PTATLAS=ATLAS FOUND: libraries = ['ptf77blas', 'ptcblas', 'atlas'] librarydirs = ['/hosts/nas1/shares/maxa/home/mzhou/bin/lib'] language = c

/tmpmnt/nas1/shares/maxa/home/mzhou/numpy-1.4.1rc3/numpy/distutils/command/config.py:394: DeprecationWarning: +++++++++++++++++++++++++++++++++++++++++++++++++ Usage of getoutput is deprecated: please do not use it anymore, and avoid configuration checks involving running executable on the target machine. +++++++++++++++++++++++++++++++++++++++++++++++++

DeprecationWarning) customize GnuFCompiler Found executable /usr/bin/g77 gnu: no Fortran 90 compiler found Could not locate executable $(FORTRAN) gnu: no Fortran 90 compiler found customize GnuFCompiler gnu: no Fortran 90 compiler found gnu: no Fortran 90 compiler found customize GnuFCompiler using config compiling '_configtest.c':

/* This file is generated from numpy/distutils/systeminfo.py */ void ATLbuildinfo(void); int main(void) { ATL_buildinfo(); return 0; } C compiler: gcc -DNDEBUG -g -O3 -Wall -Wstrict-prototypes -O3 -Wall -pedantic -static $(HDRS) $(DEFINES) -fPIC

compile options: '-c' gcc: configtest.c sh: HDRS: command not found sh: DEFINES: command not found gcc _configtest.o -L/hosts/nas1/shares/maxa/home/mzhou/bin/lib -lptf77blas -lptcblas -latlas -o _configtest /hosts/nas1/shares/maxa/home/mzhou/bin/lib/libatlas.so: undefined reference to pthread_attr_setaffinity_np' collect2: ld returned 1 exit status /hosts/nas1/shares/maxa/home/mzhou/bin/lib/libatlas.so: undefined reference topthreadattrsetaffinitynp' collect2: ld returned 1 exit status failure. removing: configtest.c _configtest.o Status: 255 Output: FOUND: libraries = ['ptf77blas', 'ptcblas', 'atlas'] librarydirs = ['/hosts/nas1/shares/maxa/home/mzhou/bin/lib'] language = c definemacros = [('NOATLAS_INFO', 2)]

lapackoptinfo: lapackmklinfo: mkl_info: libraries mkl,vml,guide not found in /hosts/nas1/shares/maxa/home/mzhou/bin/lib NOT AVAILABLE

NOT AVAILABLE

atlasthreadsinfo: Setting PTATLAS=ATLAS libraries lapackatlas not found in /hosts/nas1/shares/maxa/home/mzhou/bin/lib numpy.distutils.systeminfo.atlasthreadsinfo Setting PTATLAS=ATLAS Setting PTATLAS=ATLAS FOUND: libraries = ['lapack', 'ptf77blas', 'ptcblas', 'atlas'] library_dirs = ['/hosts/nas1/shares/maxa/home/mzhou/bin/lib'] language = f77

customize GnuFCompiler gnu: no Fortran 90 compiler found gnu: no Fortran 90 compiler found customize GnuFCompiler gnu: no Fortran 90 compiler found gnu: no Fortran 90 compiler found customize GnuFCompiler using config compiling '_configtest.c':

/* This file is generated from numpy/distutils/systeminfo.py */ void ATLbuildinfo(void); int main(void) { ATL_buildinfo(); return 0; } C compiler: gcc -DNDEBUG -g -O3 -Wall -Wstrict-prototypes -O3 -Wall -pedantic -static $(HDRS) $(DEFINES) -fPIC

compile options: '-c' gcc: configtest.c sh: HDRS: command not found sh: DEFINES: command not found gcc _configtest.o -L/hosts/nas1/shares/maxa/home/mzhou/bin/lib -llapack -lptf77blas -lptcblas -latlas -o _configtest /hosts/nas1/shares/maxa/home/mzhou/bin/lib/libatlas.so: undefined reference to pthread_attr_setaffinity_np' collect2: ld returned 1 exit status /hosts/nas1/shares/maxa/home/mzhou/bin/lib/libatlas.so: undefined reference topthreadattrsetaffinitynp' collect2: ld returned 1 exit status failure. removing: configtest.c _configtest.o Status: 255 Output: FOUND: libraries = ['lapack', 'ptf77blas', 'ptcblas', 'atlas'] librarydirs = ['/hosts/nas1/shares/maxa/home/mzhou/bin/lib'] language = f77 definemacros = [('NOATLAS_INFO', 2)]

running build running configcc unifing configcc, config, buildclib, buildext, build commands --compiler options running configfc unifing configfc, config, buildclib, buildext, build commands --fcompiler options running buildsrc buildsrc building py_modules sources building library "npymath" sources customize GnuFCompiler gnu: no Fortran 90 compiler found gnu: no Fortran 90 compiler found customize GnuFCompiler gnu: no Fortran 90 compiler found gnu: no Fortran 90 compiler found customize GnuFCompiler using config C compiler: gcc -DNDEBUG -g -O3 -Wall -Wstrict-prototypes -O3 -Wall -pedantic -static $(HDRS) $(DEFINES) -fPIC

compile options: '-Inumpy/core/src/private -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/include -I//hosts/nas1/shares/maxa/home/mzhou/bin/include/python2.6 -c' gcc: _configtest.c sh: HDRS: command not found sh: DEFINES: command not found gcc _configtest.o -o _configtest success! removing: _configtest.c _configtest.o _configtest C compiler: gcc -DNDEBUG -g -O3 -Wall -Wstrict-prototypes -O3 -Wall -pedantic -static $(HDRS) $(DEFINES) -fPIC

compile options: '-Inumpy/core/src/private -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/include -I//hosts/nas1/shares/maxa/home/mzhou/bin/include/python2.6 -c' gcc: _configtest.c sh: HDRS: command not found sh: DEFINES: command not found _configtest.c:1: warning: conflicting types for built-in function 'exp' gcc _configtest.o -o _configtest _configtest.o(.text+0x5): In function main': /hosts/nas1/shares/maxa/home/mzhou/numpy-1.4.1rc3/_configtest.c:6: undefined reference toexp' collect2: ld returned 1 exit status _configtest.o(.text+0x5): In function main': /hosts/nas1/shares/maxa/home/mzhou/numpy-1.4.1rc3/_configtest.c:6: undefined reference toexp' collect2: ld returned 1 exit status failure. removing: _configtest.c _configtest.o C compiler: gcc -DNDEBUG -g -O3 -Wall -Wstrict-prototypes -O3 -Wall -pedantic -static $(HDRS) $(DEFINES) -fPIC

compile options: '-Inumpy/core/src/private -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/include -I//hosts/nas1/shares/maxa/home/mzhou/bin/include/python2.6 -c' gcc: configtest.c sh: HDRS: command not found sh: DEFINES: command not found _configtest.c:1: warning: conflicting types for built-in function 'exp' gcc _configtest.o -lm -o _configtest success! removing: _configtest.c _configtest.o _configtest building extension "numpy.core.sort" sources Generating build/src.linux-x86_64-2.6/numpy/core/include/numpy/config.h C compiler: gcc -DNDEBUG -g -O3 -Wall -Wstrict-prototypes -O3 -Wall -pedantic -static $(HDRS) $(DEFINES) -fPIC

compile options: '-Inumpy/core/src/private -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/include -I//hosts/nas1/shares/maxa/home/mzhou/bin/include/python2.6 -c' gcc: configtest.c sh: HDRS: command not found sh: DEFINES: command not found In file included from //hosts/nas1/shares/maxa/home/mzhou/bin/include/python2.6/Python.h:58, from _configtest.c:1: //hosts/nas1/shares/maxa/home/mzhou/bin/include/python2.6/pyport.h:685:2: #error "LONGBIT definition appears wrong for platform (bad gcc/glibc config?)." In file included from //hosts/nas1/shares/maxa/home/mzhou/bin/include/python2.6/Python.h:86, from configtest.c:1: //hosts/nas1/shares/maxa/home/mzhou/bin/include/python2.6/intobject.h:45: warning: ISO C90 does not support long long' In file included from //hosts/nas1/shares/maxa/home/mzhou/bin/include/python2.6/Python.h:88, from _configtest.c:1: //hosts/nas1/shares/maxa/home/mzhou/bin/include/python2.6/longobject.h:47: warning: ISO C90 does not supportlong long' //hosts/nas1/shares/maxa/home/mzhou/bin/include/python2.6/longobject.h:48: warning: ISO C90 does not support long long' //hosts/nas1/shares/maxa/home/mzhou/bin/include/python2.6/longobject.h:49: warning: ISO C90 does not supportlong long' //hosts/nas1/shares/maxa/home/mzhou/bin/include/python2.6/longobject.h:50: warning: ISO C90 does not support long long' //hosts/nas1/shares/maxa/home/mzhou/bin/include/python2.6/longobject.h:51: warning: ISO C90 does not supportlong long' sh: HDRS: command not found sh: DEFINES: command not found In file included from //hosts/nas1/shares/maxa/home/mzhou/bin/include/python2.6/Python.h:58, from _configtest.c:1: //hosts/nas1/shares/maxa/home/mzhou/bin/include/python2.6/pyport.h:685:2: #error "LONGBIT definition appears wrong for platform (bad gcc/glibc config?)." In file included from //hosts/nas1/shares/maxa/home/mzhou/bin/include/python2.6/Python.h:86, from configtest.c:1: //hosts/nas1/shares/maxa/home/mzhou/bin/include/python2.6/intobject.h:45: warning: ISO C90 does not support long long' In file included from //hosts/nas1/shares/maxa/home/mzhou/bin/include/python2.6/Python.h:88, from _configtest.c:1: //hosts/nas1/shares/maxa/home/mzhou/bin/include/python2.6/longobject.h:47: warning: ISO C90 does not supportlong long' //hosts/nas1/shares/maxa/home/mzhou/bin/include/python2.6/longobject.h:48: warning: ISO C90 does not support long long' //hosts/nas1/shares/maxa/home/mzhou/bin/include/python2.6/longobject.h:49: warning: ISO C90 does not supportlong long' //hosts/nas1/shares/maxa/home/mzhou/bin/include/python2.6/longobject.h:50: warning: ISO C90 does not support long long' //hosts/nas1/shares/maxa/home/mzhou/bin/include/python2.6/longobject.h:51: warning: ISO C90 does not supportlong long' failure. removing: _configtest.c _configtest.o Traceback (most recent call last): File "setup.py", line 187, in <module> setuppackage() File "setup.py", line 180, in setuppackage configuration=configuration ) File "/tmpmnt/nas1/shares/maxa/home/mzhou/numpy-1.4.1rc3/numpy/distutils/core.py", line 186, in setup return oldsetup(**newattr) File "//hosts/nas1/shares/maxa/home/mzhou/bin/lib/python2.6/distutils/core.py", line 152, in setup dist.runcommands() File "//hosts/nas1/shares/maxa/home/mzhou/bin/lib/python2.6/distutils/dist.py", line 975, in runcommands self.runcommand(cmd) File "//hosts/nas1/shares/maxa/home/mzhou/bin/lib/python2.6/distutils/dist.py", line 995, in runcommand cmdobj.run() File "/tmpmnt/nas1/shares/maxa/home/mzhou/numpy-1.4.1rc3/numpy/distutils/command/build.py", line 37, in run oldbuild.run(self) File "//hosts/nas1/shares/maxa/home/mzhou/bin/lib/python2.6/distutils/command/build.py", line 134, in run self.runcommand(cmdname) File "//hosts/nas1/shares/maxa/home/mzhou/bin/lib/python2.6/distutils/cmd.py", line 333, in runcommand self.distribution.runcommand(command) File "//hosts/nas1/shares/maxa/home/mzhou/bin/lib/python2.6/distutils/dist.py", line 995, in runcommand cmdobj.run() File "/tmpmnt/nas1/shares/maxa/home/mzhou/numpy-1.4.1rc3/numpy/distutils/command/buildsrc.py", line 152, in run self.buildsources() File "/tmpmnt/nas1/shares/maxa/home/mzhou/numpy-1.4.1rc3/numpy/distutils/command/buildsrc.py", line 169, in buildsources self.buildextensionsources(ext) File "/tmpmnt/nas1/shares/maxa/home/mzhou/numpy-1.4.1rc3/numpy/distutils/command/buildsrc.py", line 328, in buildextensionsources sources = self.generatesources(sources, ext) File "/tmpmnt/nas1/shares/maxa/home/mzhou/numpy-1.4.1rc3/numpy/distutils/command/buildsrc.py", line 385, in generatesources source = func(extension, builddir) File "numpy/core/setup.py", line 381, in generateconfigh moredefs, ignored = cocache.checktypes(configcmd, ext, builddir) File "numpy/core/setup.py", line 41, in checktypes out = checktypes(*a, **kw) File "numpy/core/setup.py", line 246, in checktypes "Cannot compiler 'Python.h'. Perhaps you need to "\ SystemError: Cannot compiler 'Python.h'. Perhaps you need to install python-dev|python-devel.