Hi, Does anyone have experience building SciPy on 64 bit linux boxes? Our machine is a dual Opteron, running something like RedHat Enterprise 4.2: xxi1 : 74>uname -a Linux xxi1.nrl.navy.mil 2.6.9-11.ELsmp #1 SMP Thu Jun 16 11:18:13 CDT 2005 x86_64 x86_64 x86_64 GNU/Linux We've been running into problems with numpy/scipy looking for libraries in /usr/lib when it should be using /usr/lib64, so that a simple install with setup.py install doesn't work. It crashes when you run and it loads those 32 bit libraries. I think all I need to do is ensure that the library search paths include /usr/lib64 and / usr/X11R6/lib64 and NOT /usr/lib or /usr/X11R6/lib. What is the easy or "right" way to do this? Is there an option to setup.py? Should I make a site.cfg (and where should it reside?)? Should I edit system_info.py? I assume that this configuration is becoming more common as 64-bit processors show up in more machines, so I'm surprised that setup.py doesn't already figure it out and "do the right thing". Are we doing something boneheaded? Thanks, -- Paul
Let me ask you this: do you have Python itself built in 64 bit? When I tried that here on my AIX server, I could not get the datetime module to build. Mark F. Morss Principal Analyst, Market Risk American Electric Power Paul Ray <Paul.Ray@nrl.nav y.mil> To Sent by: SciPy Users List scipy-user-bounce <scipy-user@scipy.net> s@scipy.net cc Dan Wood <dwood@ssd5.nrl.navy.mil> Subject 03/06/2006 07:13 [SciPy-user] 64 bit support PM Please respond to SciPy Users List <scipy-user@scipy .net> Hi, Does anyone have experience building SciPy on 64 bit linux boxes? Our machine is a dual Opteron, running something like RedHat Enterprise 4.2: xxi1 : 74>uname -a Linux xxi1.nrl.navy.mil 2.6.9-11.ELsmp #1 SMP Thu Jun 16 11:18:13 CDT 2005 x86_64 x86_64 x86_64 GNU/Linux We've been running into problems with numpy/scipy looking for libraries in /usr/lib when it should be using /usr/lib64, so that a simple install with setup.py install doesn't work. It crashes when you run and it loads those 32 bit libraries. I think all I need to do is ensure that the library search paths include /usr/lib64 and / usr/X11R6/lib64 and NOT /usr/lib or /usr/X11R6/lib. What is the easy or "right" way to do this? Is there an option to setup.py? Should I make a site.cfg (and where should it reside?)? Should I edit system_info.py? I assume that this configuration is becoming more common as 64-bit processors show up in more machines, so I'm surprised that setup.py doesn't already figure it out and "do the right thing". Are we doing something boneheaded? Thanks, -- Paul _______________________________________________ SciPy-user mailing list SciPy-user@scipy.net http://www.scipy.net/mailman/listinfo/scipy-user
On 7 Mar 2006, at 00:13, Paul Ray wrote:
Hi,
Does anyone have experience building SciPy on 64 bit linux boxes?
Our machine is a dual Opteron, running something like RedHat Enterprise 4.2: xxi1 : 74>uname -a Linux xxi1.nrl.navy.mil 2.6.9-11.ELsmp #1 SMP Thu Jun 16 11:18:13 CDT 2005 x86_64 x86_64 x86_64 GNU/Linux
We've been running into problems with numpy/scipy looking for libraries in /usr/lib when it should be using /usr/lib64, so that a simple install with setup.py install doesn't work. It crashes when you run and it loads those 32 bit libraries. I think all I need to do is ensure that the library search paths include /usr/lib64 and / usr/X11R6/lib64 and NOT /usr/lib or /usr/X11R6/lib. What is the easy or "right" way to do this? Is there an option to setup.py? Should I make a site.cfg (and where should it reside?)? Should I edit system_info.py?
I assume that this configuration is becoming more common as 64-bit processors show up in more machines, so I'm surprised that setup.py doesn't already figure it out and "do the right thing". Are we doing something boneheaded?
I managed to get numpy/scipy/matplotlib set up on a single core (SUN) Opteron running a similar RedHat uname -a Linux nohow 2.6.9-22.0.2.EL #1 Thu Jan 5 17:03:08 EST 2006 x86_64 x86_64 x86_64 GNU/Linux (BTW - was the uname -a issued last summer, or is your clock wrong:) I'm sure that I did not do it the easy way -- i used a site.cfg -- but it worked in the end. Since I do not have root privileges on this computer, and in any case I used the acml libraries, I used a site.cfg file for numpy and scipy. I believe that the code has been changed to allow this site.cfg file to reside either in (in decreasing order of priority) 1. the directory where you are doing setup.py from 2. your home directory $HOME 3. the numpy/distutils subdirectory of the root numpy source directory when installing numpy OR (when installing scipy) the distutils subdirectory of the *installed* numpy directory. This copying of the site.cfg is now automatically done when numpy is installed. numpy and scipy only seemed to need the site.cfg file to find the acml libraries (or in your case, presumably the Atlas libraries). The standard setup.py worked fine otherwise. FFTW of course has to be set, so that $FFTW/include and $FFTW/lib hold the include files and fftw libraries. For matplotlib, I did have to modfy the setupext.py file, replacing libdirs = [os.path.join(p, 'lib') for p in basedir [sys.platform] if os.path.exists(p)] by libdirs = [os.path.join(p, 'lib64') for p in basedir [sys.platform] if os.path.exists(p)] + \ [os.path.join(p, 'lib') for p in basedir[sys.platform] if os.path.exists(p)] in function add_base_flags (~line 104) HTH. George.
George Nurser wrote:
On 7 Mar 2006, at 00:13, Paul Ray wrote:
Hi,
Does anyone have experience building SciPy on 64 bit linux boxes?
Our machine is a dual Opteron, running something like RedHat Enterprise 4.2: xxi1 : 74>uname -a Linux xxi1.nrl.navy.mil 2.6.9-11.ELsmp #1 SMP Thu Jun 16 11:18:13 CDT 2005 x86_64 x86_64 x86_64 GNU/Linux
We've been running into problems with numpy/scipy looking for libraries in /usr/lib when it should be using /usr/lib64, so that a simple install with setup.py install doesn't work. It crashes when you run and it loads those 32 bit libraries. I think all I need to do is ensure that the library search paths include /usr/lib64 and / usr/X11R6/lib64 and NOT /usr/lib or /usr/X11R6/lib. What is the easy or "right" way to do this? Is there an option to setup.py? Should I make a site.cfg (and where should it reside?)? Should I edit system_info.py?
I assume that this configuration is becoming more common as 64-bit processors show up in more machines, so I'm surprised that setup.py doesn't already figure it out and "do the right thing". Are we doing something boneheaded?
I managed to get numpy/scipy/matplotlib set up on a single core (SUN) Opteron running a similar RedHat uname -a Linux nohow 2.6.9-22.0.2.EL #1 Thu Jan 5 17:03:08 EST 2006 x86_64 x86_64 x86_64 GNU/Linux (BTW - was the uname -a issued last summer, or is your clock wrong:)
I'm sure that I did not do it the easy way -- i used a site.cfg -- but it worked in the end.
Since I do not have root privileges on this computer, and in any case I used the acml libraries, I used a site.cfg file for numpy and scipy.
I believe that the code has been changed to allow this site.cfg file to reside either in (in decreasing order of priority) 1. the directory where you are doing setup.py from 2. your home directory $HOME 3. the numpy/distutils subdirectory of the root numpy source directory when installing numpy OR (when installing scipy) the distutils subdirectory of the *installed* numpy directory. This copying of the site.cfg is now automatically done when numpy is installed.
numpy and scipy only seemed to need the site.cfg file to find the acml libraries (or in your case, presumably the Atlas libraries). The standard setup.py worked fine otherwise. FFTW of course has to be set, so that $FFTW/include and $FFTW/lib hold the include files and fftw libraries.
For matplotlib, I did have to modfy the setupext.py file, replacing libdirs = [os.path.join(p, 'lib') for p in basedir [sys.platform] if os.path.exists(p)] by libdirs = [os.path.join(p, 'lib64') for p in basedir [sys.platform] if os.path.exists(p)] + \ [os.path.join(p, 'lib') for p in basedir[sys.platform] if os.path.exists(p)] in function add_base_flags (~line 104)
HTH. George.
_______________________________________________ SciPy-user mailing list SciPy-user@scipy.net http://www.scipy.net/mailman/listinfo/scipy-user
Hi George, Please can you send me your site.cfg. And how did you set FFTW ? I look forward to hearing from you. Nils
participants (4)
-
George Nurser -
mfmorss＠aep.com -
Nils Wagner -
Paul Ray