Linux numpy 1.0.1 install failed
Hi List, I am trying to install numpy 1.0.1 on Linux. (Numeric and numarray have been fine) System info: Redhat Linux kernel 2.4 with gcc 3.2.3 but no separate FORTRAN compiler. It has a Fortran 77 compiler (the one which comes as part of gcc) My questions: 1) install can't find ATLAS (*.a) that I specify. Do they have to be *.so files? Do the *.a file sizes look right? Where can I get libblas.so liblapack.so files? 2) do I need a FORTRAN compiler? Will Fortran 77 compiler do? Thanks, Shawn Followings are error messages: ----------------------------- When I type "python setup.py install > numpy.out", I get: Screen display as follows: ----------------------------- Running from numpy source directory. /home/sgong/dev/numpy-1.0.1/numpy/distutils/system_info.py:934: UserWarning: ********************************************************************* Lapack library (from ATLAS) is probably incomplete: size of /usr/lib/liblapack.so is 3676k (expected >4000k) Follow the instructions in the KNOWN PROBLEMS section of the file numpy/INSTALL.txt. ********************************************************************* I then asked system admin people to install a complete ATLAS onto /usr/local/lib/atlas -rw-r--r-- 1 root root 8049172 May 15 08:49 libatlas.a -rw-r--r-- 1 root root 279016 May 15 08:49 libcblas.a -rw-r--r-- 1 root root 342062 May 15 08:49 libf77blas.a -rw-r--r-- 1 root root 5314268 May 15 08:49 liblapack.a -rw-r--r-- 1 root root 279590 May 15 08:49 libptcblas.a -rw-r--r-- 1 root root 342430 May 15 08:49 libptf77blas.a -rw-r--r-- 1 root root 320316 May 15 08:49 libtstatlas.a System admin people said that he doesn't know how to get/install *.so. He can only get *.a library. I also changed site.cfg to enter "library_dirs = /usr/local/lib/atlas/" Please find the numpy.out.txt file. Some of the lines are: -------------------------------- F2PY Version 2_3473 blas_opt_info: blas_mkl_info: libraries mkl,vml,guide not found in /home/sgong/dev/dist/lib libraries mkl,vml,guide not found in /usr/local/lib libraries mkl,vml,guide not found in /usr/lib NOT AVAILABLE atlas_blas_threads_info: Setting PTATLAS=ATLAS libraries lapack,blas not found in /usr/local/lib/atlas libraries lapack,blas not found in /usr/local/lib/atlas/ libraries lapack,blas not found in /home/sgong/dev/dist/lib libraries lapack,blas not found in /usr/local/lib/atlas libraries lapack,blas not found in /usr/local/lib Setting PTATLAS=ATLAS Setting PTATLAS=ATLAS FOUND: libraries = ['lapack', 'blas'] library_dirs = ['/usr/lib'] language = c Could not locate executable gfortran Could not locate executable f95 customize GnuFCompiler customize GnuFCompiler customize GnuFCompiler using config compiling '_configtest.c': /* This file is generated from numpy_distutils/system_info.py */ void ATL_buildinfo(void); int main(void) { ATL_buildinfo(); return 0; } C compiler: gcc -fno-strict-aliasing -DNDEBUG -g -O3 -Wall -Wstrict-prototypes -fPIC compile options: '-c' gcc: _configtest.c gcc _configtest.o -L/usr/lib -llapack -lblas -o _configtest _configtest.o(.text+0x15): In function `main': /home/sgong/dev/numpy-1.0.1/_configtest.c:5: undefined reference to `ATL_buildinfo' /usr/lib/liblapack.so: undefined reference to `e_wsfe' /usr/lib/liblapack.so: undefined reference to `z_abs' /usr/lib/liblapack.so: undefined reference to `c_sqrt' /usr/lib/liblapack.so: undefined reference to `s_cmp' /usr/lib/liblapack.so: undefined reference to `z_exp' /usr/lib/liblapack.so: undefined reference to `c_exp' /usr/lib/liblapack.so: undefined reference to `etime_' /usr/lib/liblapack.so: undefined reference to `do_fio' /usr/lib/liblapack.so: undefined reference to `z_sqrt' /usr/lib/liblapack.so: undefined reference to `s_cat' /usr/lib/liblapack.so: undefined reference to `s_stop' /usr/lib/liblapack.so: undefined reference to `c_abs' /usr/lib/liblapack.so: undefined reference to `s_wsfe' /usr/lib/liblapack.so: undefined reference to `s_copy' collect2: ld returned 1 exit status _configtest.o(.text+0x15): In function `main': /home/sgong/dev/numpy-1.0.1/_configtest.c:5: undefined reference to `ATL_buildinfo'
Gong, Shawn (Contractor) wrote:
Hi List,
I am trying to install numpy 1.0.1 on Linux. (Numeric and numarray have been fine) System info: Redhat Linux kernel 2.4 with gcc 3.2.3 but no separate FORTRAN compiler. It has a Fortran 77 compiler (the one which comes as part of gcc)
My questions: 1) install can't find ATLAS (*.a) that I specify. Do they have to be *.so files?
No.
Do the *.a file sizes look right?
Pretty much.
Where can I get libblas.so liblapack.so files?
Don't bother. Try to get the libraries that you have working; see below.
2) do I need a FORTRAN compiler? Will Fortran 77 compiler do?
Yes. Yes.
I also changed site.cfg to enter "library_dirs = /usr/local/lib/atlas/"
Could you provide the complete site.cfg file and tell us where you put it relative to the numpy source directory? -- Robert Kern "I have come to believe that the whole world is an enigma, a harmless enigma that is made terrible by our own mad attempt to interpret it as though it had an underlying truth." -- Umberto Eco
Thank you Robert for the quick reply. I have been fighting this for a while. site.cfg file is attached. It is sitting in my development dir called /home/sgong/dev/numpy-1.0.1/ (same as setup.py) Shawn -----Original Message----- From: numpy-discussion-bounces@scipy.org [mailto:numpy-discussion-bounces@scipy.org] On Behalf Of Robert Kern Sent: Friday, May 18, 2007 3:59 PM To: Discussion of Numerical Python Subject: Re: [Numpy-discussion] Linux numpy 1.0.1 install failed Gong, Shawn (Contractor) wrote:
Hi List,
I am trying to install numpy 1.0.1 on Linux. (Numeric and numarray have been fine) System info: Redhat Linux kernel 2.4 with gcc 3.2.3 but no separate FORTRAN compiler. It has a Fortran 77 compiler (the one which comes as part of gcc)
My questions: 1) install can't find ATLAS (*.a) that I specify. Do they have to be *.so files?
No.
Do the *.a file sizes look right?
Pretty much.
Where can I get libblas.so liblapack.so files?
Don't bother. Try to get the libraries that you have working; see below.
2) do I need a FORTRAN compiler? Will Fortran 77 compiler do?
Yes. Yes.
I also changed site.cfg to enter "library_dirs = /usr/local/lib/atlas/"
Could you provide the complete site.cfg file and tell us where you put it relative to the numpy source directory? -- Robert Kern "I have come to believe that the whole world is an enigma, a harmless enigma that is made terrible by our own mad attempt to interpret it as though it had an underlying truth." -- Umberto Eco _______________________________________________ Numpy-discussion mailing list Numpy-discussion@scipy.org http://projects.scipy.org/mailman/listinfo/numpy-discussion
Gong, Shawn (Contractor) wrote:
Thank you Robert for the quick reply. I have been fighting this for a while.
site.cfg file is attached. It is sitting in my development dir called /home/sgong/dev/numpy-1.0.1/ (same as setup.py)
You are missing some of the ATLAS libraries. See this section in the site.cfg.example (I don't recall if it made it into 1.0.1): # Defaults # ======== # The settings given here will apply to all other sections if not overridden. # This is a good place to add general library and include directories like # /usr/local/{lib,include} # #[DEFAULT] #library_dirs = /usr/local/lib #include_dirs = /usr/local/include # Optimized BLAS and LAPACK # ------------------------- # Use the blas_opt and lapack_opt sections to give any settings that are # required to link against your chosen BLAS and LAPACK, including the regular # FORTRAN reference BLAS and also ATLAS. Some other sections still exist for # linking against certain optimized libraries (e.g. [atlas], [lapack_atlas]), # however, they are now deprecated and should not be used. # # These are typical configurations for ATLAS (assuming that the library and # include directories have already been set in [DEFAULT]; the include directory # is important for the BLAS C interface): # #[blas_opt] #libraries = f77blas, cblas, atlas # #[lapack_opt] #libraries = lapack, f77blas, cblas, atlas -- Robert Kern "I have come to believe that the whole world is an enigma, a harmless enigma that is made terrible by our own mad attempt to interpret it as though it had an underlying truth." -- Umberto Eco
Hi Robert, 1) your reply: You are missing some of the ATLAS libraries. Do you mean that I need install more ATLAS libraries? What are they? These are what I have right now: -rw-r--r-- 1 root root 8049172 May 15 08:49 libatlas.a -rw-r--r-- 1 root root 279016 May 15 08:49 libcblas.a -rw-r--r-- 1 root root 342062 May 15 08:49 libf77blas.a -rw-r--r-- 1 root root 5314268 May 15 08:49 liblapack.a -rw-r--r-- 1 root root 279590 May 15 08:49 libptcblas.a -rw-r--r-- 1 root root 342430 May 15 08:49 libptf77blas.a -rw-r--r-- 1 root root 320316 May 15 08:49 libtstatlas.a 2) do I need to add more entries in site.cfg? what to add? 3) is numpy-1.0.1 too old? Should I try 1.0.2? Thanks, Shawn -----Original Message----- From: numpy-discussion-bounces@scipy.org [mailto:numpy-discussion-bounces@scipy.org] On Behalf Of Robert Kern Sent: Friday, May 18, 2007 4:09 PM To: Discussion of Numerical Python Subject: Re: [Numpy-discussion] Linux numpy 1.0.1 install failed Gong, Shawn (Contractor) wrote:
Thank you Robert for the quick reply. I have been fighting this for a while.
site.cfg file is attached. It is sitting in my development dir called /home/sgong/dev/numpy-1.0.1/ (same as setup.py)
You are missing some of the ATLAS libraries. See this section in the site.cfg.example (I don't recall if it made it into 1.0.1): # Defaults # ======== # The settings given here will apply to all other sections if not overridden. # This is a good place to add general library and include directories like # /usr/local/{lib,include} # #[DEFAULT] #library_dirs = /usr/local/lib #include_dirs = /usr/local/include # Optimized BLAS and LAPACK # ------------------------- # Use the blas_opt and lapack_opt sections to give any settings that are # required to link against your chosen BLAS and LAPACK, including the regular # FORTRAN reference BLAS and also ATLAS. Some other sections still exist for # linking against certain optimized libraries (e.g. [atlas], [lapack_atlas]), # however, they are now deprecated and should not be used. # # These are typical configurations for ATLAS (assuming that the library and # include directories have already been set in [DEFAULT]; the include directory # is important for the BLAS C interface): # #[blas_opt] #libraries = f77blas, cblas, atlas # #[lapack_opt] #libraries = lapack, f77blas, cblas, atlas -- Robert Kern "I have come to believe that the whole world is an enigma, a harmless enigma that is made terrible by our own mad attempt to interpret it as though it had an underlying truth." -- Umberto Eco _______________________________________________ Numpy-discussion mailing list Numpy-discussion@scipy.org http://projects.scipy.org/mailman/listinfo/numpy-discussion
Gong, Shawn (Contractor) wrote:
Hi Robert, 1) your reply: You are missing some of the ATLAS libraries. Do you mean that I need install more ATLAS libraries?
No, sorry, I meant that your site.cfg did not list all of the ATLAS libraries that need to be listed.
2) do I need to add more entries in site.cfg? what to add?
The [blas_opt] and [lapack_opt] sections in the example.
3) is numpy-1.0.1 too old? Should I try 1.0.2?
It would be a good idea, but not necessary. -- Robert Kern "I have come to believe that the whole world is an enigma, a harmless enigma that is made terrible by our own mad attempt to interpret it as though it had an underlying truth." -- Umberto Eco
numpy-1.0.2 (from sourceforge site) doesn't even have the site.cfg file. Is it unnecessary fro this version or it is a mistake? Shawn -----Original Message----- From: numpy-discussion-bounces@scipy.org [mailto:numpy-discussion-bounces@scipy.org] On Behalf Of Robert Kern Sent: Friday, May 18, 2007 4:24 PM To: Discussion of Numerical Python Subject: Re: [Numpy-discussion] Linux numpy 1.0.1 install failed Gong, Shawn (Contractor) wrote:
Hi Robert, 1) your reply: You are missing some of the ATLAS libraries. Do you mean that I need install more ATLAS libraries?
No, sorry, I meant that your site.cfg did not list all of the ATLAS libraries that need to be listed.
2) do I need to add more entries in site.cfg? what to add?
The [blas_opt] and [lapack_opt] sections in the example.
3) is numpy-1.0.1 too old? Should I try 1.0.2?
It would be a good idea, but not necessary. -- Robert Kern "I have come to believe that the whole world is an enigma, a harmless enigma that is made terrible by our own mad attempt to interpret it as though it had an underlying truth." -- Umberto Eco _______________________________________________ Numpy-discussion mailing list Numpy-discussion@scipy.org http://projects.scipy.org/mailman/listinfo/numpy-discussion
Gong, Shawn (Contractor) wrote:
numpy-1.0.2 (from sourceforge site) doesn't even have the site.cfg file. Is it unnecessary fro this version or it is a mistake?
The site.cfg file is something that people who are installing numpy need to write if they need to supply that information. That information will be different for each installation, so we do not supply one with false information. -- Robert Kern "I have come to believe that the whole world is an enigma, a harmless enigma that is made terrible by our own mad attempt to interpret it as though it had an underlying truth." -- Umberto Eco
participants (2)
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Gong, Shawn (Contractor)
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Robert Kern