SciPy installation problem
Dear yt users, I'm having some trouble installing SciPy. I can install yt just fine using the install script, but if I turn the option for installing SciPy on, I get the following error: creating build/temp.linux-x86_64-2.7/scipy/fftpack/src/dfftpack compile options: '-I/data/users/borm/YT/yt-x86_64/lib/python2.7/site-packages/numpy/core/include -c' f77.sh:f77: scipy/fftpack/src/dfftpack/dsint.f Cannot open file dsint.f gcc: dsint.c: No such file or directory gcc: no input files Cannot open file dsint.f gcc: dsint.c: No such file or directory gcc: no input files error: Command "/iraf/iraf/unix/hlib//f77.sh -Wall -ffixed-form -fno-second-underscore -fPIC -O3 -funroll-loops -I/data/users/borm/YT/yt-x86_64/lib/python2.7/site-packages/numpy/core/include -c -c scipy/fftpack/src/dfftpack/dsint.f -o build/temp.linux-x86_64-2.7/scipy/fftpack/src/dfftpack/dsint.o" failed with exit status 1 I've tried uncommenting the NUMPY_ARGS lines one by one as suggested in the script, but none of that seems to work. I'm using yt version 2.6.1, changeset e0906fc5b6d5, if that helps. Any ideas on how to fix this? Thanks! Cheers, Caroline _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
Hi Caroline, Hmm, I have not ever seen this before. Changing the NUMPY_ARGS to set a fake fortran compiler definitely should have fixed it, as it should then avoid compiling any of fftpack. Can you recall which version of scipy is installed by 2.6.1? -Matt On Tue, Jan 13, 2015 at 11:10 AM, Caroline Van Borm <borm@astro.rug.nl> wrote:
Dear yt users,
I'm having some trouble installing SciPy. I can install yt just fine using the install script, but if I turn the option for installing SciPy on, I get the following error:
creating build/temp.linux-x86_64-2.7/scipy/fftpack/src/dfftpack compile options: '-I/data/users/borm/YT/yt-x86_64/lib/python2.7/site-packages/numpy/core/include -c' f77.sh:f77: scipy/fftpack/src/dfftpack/dsint.f Cannot open file dsint.f gcc: dsint.c: No such file or directory gcc: no input files Cannot open file dsint.f gcc: dsint.c: No such file or directory gcc: no input files error: Command "/iraf/iraf/unix/hlib//f77.sh -Wall -ffixed-form -fno-second-underscore -fPIC -O3 -funroll-loops -I/data/users/borm/YT/yt-x86_64/lib/python2.7/site-packages/numpy/core/include -c -c scipy/fftpack/src/dfftpack/dsint.f -o build/temp.linux-x86_64-2.7/scipy/fftpack/src/dfftpack/dsint.o" failed with exit status 1
I've tried uncommenting the NUMPY_ARGS lines one by one as suggested in the script, but none of that seems to work. I'm using yt version 2.6.1, changeset e0906fc5b6d5, if that helps.
Any ideas on how to fix this? Thanks!
Cheers, Caroline
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Hi Caroline Not sure this will help, but I in the installation script. It might help to change the scipy version it downloads from 0.12 to 0.14 by editing the scipy version line. Other than that. From my experience from using the install script, I find that the installation can succeed or fail depending on what fortran compiler you are using. Try unloading and loading a different module on your cluster, or change the relevent enviroment variables. I can help out a bit more in a few hours after these seminar sessions if you are still having problems with the installation. Ben On 14 Jan 2015 16:26, "Matthew Turk" <matthewturk@gmail.com> wrote:
Hi Caroline,
Hmm, I have not ever seen this before. Changing the NUMPY_ARGS to set a fake fortran compiler definitely should have fixed it, as it should then avoid compiling any of fftpack. Can you recall which version of scipy is installed by 2.6.1?
-Matt
On Tue, Jan 13, 2015 at 11:10 AM, Caroline Van Borm <borm@astro.rug.nl> wrote:
Dear yt users,
I'm having some trouble installing SciPy. I can install yt just fine using the install script, but if I turn the option for installing SciPy on, I get the following error:
creating build/temp.linux-x86_64-2.7/scipy/fftpack/src/dfftpack compile options: '-I/data/users/borm/YT/yt-x86_64/lib/python2.7/site-packages/numpy/core/include -c' f77.sh:f77: scipy/fftpack/src/dfftpack/dsint.f Cannot open file dsint.f gcc: dsint.c: No such file or directory gcc: no input files Cannot open file dsint.f gcc: dsint.c: No such file or directory gcc: no input files error: Command "/iraf/iraf/unix/hlib//f77.sh -Wall -ffixed-form -fno-second-underscore -fPIC -O3 -funroll-loops -I/data/users/borm/YT/yt-x86_64/lib/python2.7/site-packages/numpy/core/include -c -c scipy/fftpack/src/dfftpack/dsint.f -o build/temp.linux-x86_64-2.7/scipy/fftpack/src/dfftpack/dsint.o" failed with exit status 1
I've tried uncommenting the NUMPY_ARGS lines one by one as suggested in the script, but none of that seems to work. I'm using yt version 2.6.1, changeset e0906fc5b6d5, if that helps.
Any ideas on how to fix this? Thanks!
Cheers, Caroline
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Hi Matt, It's installing 'scipy-0.12.0', so I guess the version would be 0.12.0? By the way, when I use the option --fcompiler=gnu95, the error is the same as what I wrote previously, and when I use the option --fcompiler=fake, I get a different error: Installing numpy-1.7.1 (arguments: '--fcompiler=fake') Installing scipy-0.12.0 (arguments: '--fcompiler=fake') ******************************************** FAILURE REPORT: ******************************************** copying scipy/weave/base_info.py -> build/lib.linux-x86_64-2.7/scipy/weave creating build/lib.linux-x86_64-2.7/scipy/_build_utils copying scipy/_build_utils/_fortran.py -> build/lib.linux-x86_64-2.7/scipy/_build_utils copying scipy/_build_utils/__init__.py -> build/lib.linux-x86_64-2.7/scipy/_build_utils running build_clib customize UnixCCompiler customize UnixCCompiler using build_clib don't know how to compile Fortran code on platform 'posix' with 'fake' compiler. Supported compilers are: intelvem,none,absoft,compaq,intel,gnu,sun,nag,pathf95,ibm,gnu95,intelv,g95,intele,vast,lahey,pg,mips,hpux,intelev,intelem) building 'dfftpack' library error: library dfftpack has Fortran sources but no Fortran compiler found Thanks! Cheers, Caroline On 01/14/2015 01:05 PM, Matthew Turk wrote:
Hi Caroline,
Hmm, I have not ever seen this before. Changing the NUMPY_ARGS to set a fake fortran compiler definitely should have fixed it, as it should then avoid compiling any of fftpack. Can you recall which version of scipy is installed by 2.6.1?
-Matt
On Tue, Jan 13, 2015 at 11:10 AM, Caroline Van Borm <borm@astro.rug.nl <mailto:borm@astro.rug.nl>> wrote:
Dear yt users,
I'm having some trouble installing SciPy. I can install yt just fine using the install script, but if I turn the option for installing SciPy on, I get the following error:
creating build/temp.linux-x86_64-2.7/scipy/fftpack/src/dfftpack compile options: '-I/data/users/borm/YT/yt-x86_64/lib/python2.7/site-packages/numpy/core/include -c' f77.sh:f77: scipy/fftpack/src/dfftpack/dsint.f Cannot open file dsint.f gcc: dsint.c: No such file or directory gcc: no input files Cannot open file dsint.f gcc: dsint.c: No such file or directory gcc: no input files error: Command "/iraf/iraf/unix/hlib//f77.sh -Wall -ffixed-form -fno-second-underscore -fPIC -O3 -funroll-loops -I/data/users/borm/YT/yt-x86_64/lib/python2.7/site-packages/numpy/core/include -c -c scipy/fftpack/src/dfftpack/dsint.f -o build/temp.linux-x86_64-2.7/scipy/fftpack/src/dfftpack/dsint.o" failed with exit status 1
I've tried uncommenting the NUMPY_ARGS lines one by one as suggested in the script, but none of that seems to work. I'm using yt version 2.6.1, changeset e0906fc5b6d5, if that helps.
Any ideas on how to fix this? Thanks!
Cheers, Caroline
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Hi Caroline, Is this on OS X? If so, I think in the past at least the installer has had some trouble installing scipy. What works for me is to not install scipy through the installer, then after yt is installed, activate yt, and then type:
pip install scipy
cheers, desika On Tue, Jan 13, 2015 at 12:10 PM, Caroline Van Borm <borm@astro.rug.nl> wrote:
Dear yt users,
I'm having some trouble installing SciPy. I can install yt just fine using the install script, but if I turn the option for installing SciPy on, I get the following error:
creating build/temp.linux-x86_64-2.7/scipy/fftpack/src/dfftpack compile options: '-I/data/users/borm/YT/yt-x86_64/lib/python2.7/site-packages/numpy/core/include -c' f77.sh:f77: scipy/fftpack/src/dfftpack/dsint.f Cannot open file dsint.f gcc: dsint.c: No such file or directory gcc: no input files Cannot open file dsint.f gcc: dsint.c: No such file or directory gcc: no input files error: Command "/iraf/iraf/unix/hlib//f77.sh -Wall -ffixed-form -fno-second-underscore -fPIC -O3 -funroll-loops -I/data/users/borm/YT/yt-x86_64/lib/python2.7/site-packages/numpy/core/include -c -c scipy/fftpack/src/dfftpack/dsint.f -o build/temp.linux-x86_64-2.7/scipy/fftpack/src/dfftpack/dsint.o" failed with exit status 1
I've tried uncommenting the NUMPY_ARGS lines one by one as suggested in the script, but none of that seems to work. I'm using yt version 2.6.1, changeset e0906fc5b6d5, if that helps.
Any ideas on how to fix this? Thanks!
Cheers, Caroline
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
I suspect this is a side-effect of the iraf virus. I too have often run into the f77 trojan that comes to light in some (all?) iraf installations, and configure doesn't deal with it very well. On 01/13/2015 12:10 PM, Caroline Van Borm wrote:
Dear yt users,
I'm having some trouble installing SciPy. I can install yt just fine using the install script, but if I turn the option for installing SciPy on, I get the following error:
creating build/temp.linux-x86_64-2.7/scipy/fftpack/src/dfftpack compile options: '-I/data/users/borm/YT/yt-x86_64/lib/python2.7/site-packages/numpy/core/include -c' f77.sh:f77: scipy/fftpack/src/dfftpack/dsint.f Cannot open file dsint.f gcc: dsint.c: No such file or directory gcc: no input files Cannot open file dsint.f gcc: dsint.c: No such file or directory gcc: no input files error: Command "/iraf/iraf/unix/hlib//f77.sh -Wall -ffixed-form -fno-second-underscore -fPIC -O3 -funroll-loops -I/data/users/borm/YT/yt-x86_64/lib/python2.7/site-packages/numpy/core/include -c -c scipy/fftpack/src/dfftpack/dsint.f -o build/temp.linux-x86_64-2.7/scipy/fftpack/src/dfftpack/dsint.o" failed with exit status 1
I've tried uncommenting the NUMPY_ARGS lines one by one as suggested in the script, but none of that seems to work. I'm using yt version 2.6.1, changeset e0906fc5b6d5, if that helps.
Any ideas on how to fix this? Thanks!
Cheers, Caroline
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Hi all, Thank you all for your suggestions! It turns out that iraf is installed on my work desktop and it somehow changes the F77 environment variable. After changing it back to /usr/bin/f77 I was able to install SciPy. However, when I now try to do 'from scipy.integrate import odeint' for example, I get the following error message: In [2]: from scipy.interpolate import odeint --------------------------------------------------------------------------- ImportError Traceback (most recent call last) /data/users/borm/YT/yt-x86_64/src/yt-hg/scripts/iyt in <module>() ----> 1 from scipy.interpolate import odeint /data/users/borm/YT/yt-x86_64/lib/python2.7/site-packages/scipy/interpolate/__init__.py in <module>() 148 from __future__ import division, print_function, absolute_import 149 --> 150 from .interpolate import * 151 from .fitpack import * 152 /data/users/borm/YT/yt-x86_64/lib/python2.7/site-packages/scipy/interpolate/interpolate.py in <module>() 10 dot, poly1d, asarray, intp 11 import numpy as np ---> 12 import scipy.special as spec 13 import math 14 /data/users/borm/YT/yt-x86_64/lib/python2.7/site-packages/scipy/special/__init__.py in <module>() 527 from __future__ import division, print_function, absolute_import 528 --> 529 from ._ufuncs import * 530 from ._ufuncs_cxx import * 531 ImportError: /data/users/borm/YT/yt-x86_64/lib/python2.7/site-packages/scipy/special/_ufuncs.so: undefined symbol: s_stop It seems this is again related to the compiler, but I'm not sure what to do about it. I have tried once more to set the NUMPY_ARGS to the different options in the install script, and also to install yt without SciPy and then install it using 'pip install scipy', but every time I get the same error. My OS is Scientific Linux 6, by the way. Cheers, Caroline On 01/14/2015 05:32 PM, Peter Teuben wrote:
I suspect this is a side-effect of the iraf virus. I too have often run into the f77 trojan that comes to light in some (all?) iraf installations, and configure doesn't deal with it very well.
On 01/13/2015 12:10 PM, Caroline Van Borm wrote:
Dear yt users,
I'm having some trouble installing SciPy. I can install yt just fine using the install script, but if I turn the option for installing SciPy on, I get the following error:
creating build/temp.linux-x86_64-2.7/scipy/fftpack/src/dfftpack compile options: '-I/data/users/borm/YT/yt-x86_64/lib/python2.7/site-packages/numpy/core/include -c' f77.sh:f77: scipy/fftpack/src/dfftpack/dsint.f Cannot open file dsint.f gcc: dsint.c: No such file or directory gcc: no input files Cannot open file dsint.f gcc: dsint.c: No such file or directory gcc: no input files error: Command "/iraf/iraf/unix/hlib//f77.sh -Wall -ffixed-form -fno-second-underscore -fPIC -O3 -funroll-loops -I/data/users/borm/YT/yt-x86_64/lib/python2.7/site-packages/numpy/core/include -c -c scipy/fftpack/src/dfftpack/dsint.f -o build/temp.linux-x86_64-2.7/scipy/fftpack/src/dfftpack/dsint.o" failed with exit status 1
I've tried uncommenting the NUMPY_ARGS lines one by one as suggested in the script, but none of that seems to work. I'm using yt version 2.6.1, changeset e0906fc5b6d5, if that helps.
Any ideas on how to fix this? Thanks!
Cheers, Caroline
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Hi Caroline, Have you tried deleting the scipy installation and retrying from scratch? You should be able to clean up most of the old scipy installations by repeatedly running "pip uninstall scipy". If you're patient, you can also try the nuclear option of rerunning the install script from scratch. -Nathan On Mon, Jan 19, 2015 at 8:51 AM, Caroline Van Borm <borm@astro.rug.nl> wrote:
Hi all,
Thank you all for your suggestions! It turns out that iraf is installed on my work desktop and it somehow changes the F77 environment variable. After changing it back to /usr/bin/f77 I was able to install SciPy. However, when I now try to do 'from scipy.integrate import odeint' for example, I get the following error message:
In [2]: from scipy.interpolate import odeint --------------------------------------------------------------------------- ImportError Traceback (most recent call last) /data/users/borm/YT/yt-x86_64/src/yt-hg/scripts/iyt in <module>() ----> 1 from scipy.interpolate import odeint
/data/users/borm/YT/yt-x86_64/lib/python2.7/site-packages/scipy/interpolate/__init__.py in <module>() 148 from __future__ import division, print_function, absolute_import 149 --> 150 from .interpolate import * 151 from .fitpack import * 152
/data/users/borm/YT/yt-x86_64/lib/python2.7/site-packages/scipy/interpolate/interpolate.py in <module>() 10 dot, poly1d, asarray, intp 11 import numpy as np ---> 12 import scipy.special as spec 13 import math 14
/data/users/borm/YT/yt-x86_64/lib/python2.7/site-packages/scipy/special/__init__.py in <module>() 527 from __future__ import division, print_function, absolute_import 528 --> 529 from ._ufuncs import * 530 from ._ufuncs_cxx import * 531
ImportError: /data/users/borm/YT/yt-x86_64/lib/python2.7/site-packages/scipy/special/_ufuncs.so: undefined symbol: s_stop
It seems this is again related to the compiler, but I'm not sure what to do about it. I have tried once more to set the NUMPY_ARGS to the different options in the install script, and also to install yt without SciPy and then install it using 'pip install scipy', but every time I get the same error. My OS is Scientific Linux 6, by the way.
Cheers, Caroline
On 01/14/2015 05:32 PM, Peter Teuben wrote:
I suspect this is a side-effect of the iraf virus. I too have often run into the f77 trojan that comes to light in some (all?) iraf installations, and configure doesn't deal with it very well.
On 01/13/2015 12:10 PM, Caroline Van Borm wrote:
Dear yt users,
I'm having some trouble installing SciPy. I can install yt just fine using the install script, but if I turn the option for installing SciPy on, I get the following error:
creating build/temp.linux-x86_64-2.7/scipy/fftpack/src/dfftpack compile options: '-I/data/users/borm/YT/yt-x86_64/lib/python2.7/site-packages/numpy/core/include -c' f77.sh:f77: scipy/fftpack/src/dfftpack/dsint.f Cannot open file dsint.f gcc: dsint.c: No such file or directory gcc: no input files Cannot open file dsint.f gcc: dsint.c: No such file or directory gcc: no input files error: Command "/iraf/iraf/unix/hlib//f77.sh -Wall -ffixed-form -fno-second-underscore -fPIC -O3 -funroll-loops -I/data/users/borm/YT/yt-x86_64/lib/python2.7/site-packages/numpy/core/include -c -c scipy/fftpack/src/dfftpack/dsint.f -o build/temp.linux-x86_64-2.7/scipy/fftpack/src/dfftpack/dsint.o" failed with exit status 1
I've tried uncommenting the NUMPY_ARGS lines one by one as suggested in the script, but none of that seems to work. I'm using yt version 2.6.1, changeset e0906fc5b6d5, if that helps.
Any ideas on how to fix this? Thanks!
Cheers, Caroline
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Hi Nathan, I reran the install script from scratch every time, just to be safe. I think I actually may have it working now, after setting NUMPY_ARGS="--fcompiler=g77". I've tried to load and use several SciPy functions and no errors so far. Hoping it stays that way! Thanks again! Cheers, Caroline On 01/20/2015 02:38 AM, Nathan Goldbaum wrote:
Hi Caroline,
Have you tried deleting the scipy installation and retrying from scratch? You should be able to clean up most of the old scipy installations by repeatedly running "pip uninstall scipy". If you're patient, you can also try the nuclear option of rerunning the install script from scratch.
-Nathan
On Mon, Jan 19, 2015 at 8:51 AM, Caroline Van Borm <borm@astro.rug.nl <mailto:borm@astro.rug.nl>> wrote:
Hi all,
Thank you all for your suggestions! It turns out that iraf is installed on my work desktop and it somehow changes the F77 environment variable. After changing it back to /usr/bin/f77 I was able to install SciPy. However, when I now try to do 'from scipy.integrate import odeint' for example, I get the following error message:
In [2]: from scipy.interpolate import odeint --------------------------------------------------------------------------- ImportError Traceback (most recent call last) /data/users/borm/YT/yt-x86_64/src/yt-hg/scripts/iyt in <module>() ----> 1 from scipy.interpolate import odeint
/data/users/borm/YT/yt-x86_64/lib/python2.7/site-packages/scipy/interpolate/__init__.py in <module>() 148 from __future__ import division, print_function, absolute_import 149 --> 150 from .interpolate import * 151 from .fitpack import * 152
/data/users/borm/YT/yt-x86_64/lib/python2.7/site-packages/scipy/interpolate/interpolate.py in <module>() 10 dot, poly1d, asarray, intp 11 import numpy as np ---> 12 import scipy.special as spec 13 import math 14
/data/users/borm/YT/yt-x86_64/lib/python2.7/site-packages/scipy/special/__init__.py in <module>() 527 from __future__ import division, print_function, absolute_import 528 --> 529 from ._ufuncs import * 530 from ._ufuncs_cxx import * 531
ImportError: /data/users/borm/YT/yt-x86_64/lib/python2.7/site-packages/scipy/special/_ufuncs.so: undefined symbol: s_stop
It seems this is again related to the compiler, but I'm not sure what to do about it. I have tried once more to set the NUMPY_ARGS to the different options in the install script, and also to install yt without SciPy and then install it using 'pip install scipy', but every time I get the same error. My OS is Scientific Linux 6, by the way.
Cheers, Caroline
On 01/14/2015 05:32 PM, Peter Teuben wrote:
I suspect this is a side-effect of the iraf virus. I too have often run into the f77 trojan that comes to light in some (all?) iraf installations, and configure doesn't deal with it very well.
On 01/13/2015 12:10 PM, Caroline Van Borm wrote:
Dear yt users,
I'm having some trouble installing SciPy. I can install yt just fine using the install script, but if I turn the option for installing SciPy on, I get the following error:
creating build/temp.linux-x86_64-2.7/scipy/fftpack/src/dfftpack compile options: '-I/data/users/borm/YT/yt-x86_64/lib/python2.7/site-packages/numpy/core/include -c' f77.sh:f77: scipy/fftpack/src/dfftpack/dsint.f Cannot open file dsint.f gcc: dsint.c: No such file or directory gcc: no input files Cannot open file dsint.f gcc: dsint.c: No such file or directory gcc: no input files error: Command "/iraf/iraf/unix/hlib//f77.sh -Wall -ffixed-form -fno-second-underscore -fPIC -O3 -funroll-loops -I/data/users/borm/YT/yt-x86_64/lib/python2.7/site-packages/numpy/core/include -c -c scipy/fftpack/src/dfftpack/dsint.f -o build/temp.linux-x86_64-2.7/scipy/fftpack/src/dfftpack/dsint.o" failed with exit status 1
I've tried uncommenting the NUMPY_ARGS lines one by one as suggested in the script, but none of that seems to work. I'm using yt version 2.6.1, changeset e0906fc5b6d5, if that helps.
Any ideas on how to fix this? Thanks!
Cheers, Caroline
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participants (6)
-
Ben Thompson -
Caroline Van Borm -
Desika Narayanan -
Matthew Turk -
Nathan Goldbaum -
Peter Teuben