[Numpy-discussion] Numpy Installation Problem Asking
Hi, I plan to plot a sashimi plot to view the alternative splicing event of my interested gene by using MISO. After follow the following link, http://genes.mit.edu/burgelab/miso/docs/and read through the forum. Unfortunately, I still face some problems to run the complete set of MISO successful. I can run some of the python script but I still fail to run some of it :( It shown the following error message when I try some of the MISO python script (compare_miso.py, run_miso.py, sashimi_plot.py, etc). *.* *.* *.* *ImportError: No module named _ufuncs* I can successful run some of the important MISO script (index_gff.py, sam_to_bam.py). I'm downloading everything by using Python-2.7. I suspect it might due to numpy or scipy installation problem. Unfortunately, I still fail to figure it out :( I have try to use Python-3.3. But it will show the following error message when I try to run all the python script under MISO : *.* *.* *SyntaxError: invalid syntax* I have browse through forum and seqanswer etc. Unfortunately I still fail to figure out why it happen :( I have to manual download all the package and install it separately as I don't have the purposely through access network through server. It is due to the network security of server at University. Thanks and looking forward to hear from any of you. best regards edge ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] Numpy Installation Problem Asking
On Thu, Mar 20, 2014 at 4:04 PM, Chia Jing Yi cjyxiao...@gmail.com wrote: Hi, I plan to plot a sashimi plot to view the alternative splicing event of my interested gene by using MISO. After follow the following link, http://genes.mit.edu/burgelab/miso/docs/and read through the forum. Unfortunately, I still face some problems to run the complete set of MISO successful. I can run some of the python script but I still fail to run some of it :( It shown the following error message when I try some of the MISO python script (compare_miso.py, run_miso.py, sashimi_plot.py, etc). *.* *.* *.* *ImportError: No module named _ufuncs* I can successful run some of the important MISO script (index_gff.py, sam_to_bam.py). I'm downloading everything by using Python-2.7. I suspect it might due to numpy or scipy installation problem. Unfortunately, I still fail to figure it out :( I have try to use Python-3.3. But it will show the following error message when I try to run all the python script under MISO : *.* *.* *SyntaxError: invalid syntax* I have browse through forum and seqanswer etc. Unfortunately I still fail to figure out why it happen :( I have to manual download all the package and install it separately as I don't have the purposely through access network through server. It is due to the network security of server at University. Thanks and looking forward to hear from any of you. Hi, you have to give a full traceback otherwise we can't help you. And please don't double post, you sent the same message to scipy-user. Ralf ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] Numpy Installation Problem Asking
Hi, Thanks a lot for your email. I will upload the full traceback soon. Sorry for posting the same thread at scipy-user too. I don't aware about that numpy and scipy user group is linked. I apologize for my mistakes. I will be more careful in future. best regards Edge On Fri, Mar 21, 2014 at 3:37 AM, Ralf Gommers ralf.gomm...@gmail.comwrote: On Thu, Mar 20, 2014 at 4:04 PM, Chia Jing Yi cjyxiao...@gmail.comwrote: Hi, I plan to plot a sashimi plot to view the alternative splicing event of my interested gene by using MISO. After follow the following link, http://genes.mit.edu/burgelab/miso/docs/and read through the forum. Unfortunately, I still face some problems to run the complete set of MISO successful. I can run some of the python script but I still fail to run some of it :( It shown the following error message when I try some of the MISO python script (compare_miso.py, run_miso.py, sashimi_plot.py, etc). *.* *.* *.* *ImportError: No module named _ufuncs* I can successful run some of the important MISO script (index_gff.py, sam_to_bam.py). I'm downloading everything by using Python-2.7. I suspect it might due to numpy or scipy installation problem. Unfortunately, I still fail to figure it out :( I have try to use Python-3.3. But it will show the following error message when I try to run all the python script under MISO : *.* *.* *SyntaxError: invalid syntax* I have browse through forum and seqanswer etc. Unfortunately I still fail to figure out why it happen :( I have to manual download all the package and install it separately as I don't have the purposely through access network through server. It is due to the network security of server at University. Thanks and looking forward to hear from any of you. Hi, you have to give a full traceback otherwise we can't help you. And please don't double post, you sent the same message to scipy-user. Ralf ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] Numpy Installation Problem on Redhat Linux
Thank you for pointing this out. Actually I tried both --fcompiler=gnu95 and --fcompiler=gnu flags, but I got the same error message. As for the redhat version, I'm using Red Hat Enterprise Linux Server release 6.3 (Santiago). On Fri, Jul 6, 2012 at 12:42 AM, Paul Anton Letnes paul.anton.let...@gmail.com wrote: Hi, are you sure that you want g77 and not gfortran? If you want gfortran, you should pass the --fcompiler=gnu95 flag to setup.py. Which redhat version are you building on? (I don't know red hat well enough to comment, but perhaps someone else do...) Paul On 6. juli 2012, at 03:00, Hung-Hsuan Chen wrote: Dear all, I've built blas, lapack, and atlas libraries, as shown below. $ ls ~/lib/atlas/lib/ libatlas.a libcblas.a libf77blas.a liblapack.a libptcblas.a libptf77blas.a The library location are specified by site.cfg file, as shown below. [DEFAULT] library_dirs = /home/username/lib/atlas/lib include_dirs = /home/username/lib/atlas/include [blas] libraries = libf77blas, libcblas, libatlas [lapack] libraries = liblapack, libf77blas, libcblas, libatlas I've tried to build numpy (version 1.6.2) by $ python setup.py build --fcompiler=gnu However, I got the following error message: error: Command /usr/bin/g77 -g -Wall -g -Wall -shared build/temp.linux-x86_64-2.6/build/src.linux-x86_64-2.6/scipy/integrate/vodemodule.o build/temp.linux-x86_64-2.6/build/src.linux-x86_64-2.6/fortranobject.o -L/home/username/lib/ -L/usr/lib64 -Lbuild/temp.linux-x86_64-2.6 -lodepack -llinpack_lite -lmach -lblas -lpython2.6 -lg2c -o build/lib.linux-x86_64-2.6/scipy/integrate/vode.so failed with exit status I've searched internet for possible solutions whole day but don't have any progress so far. Anyone has any idea of how to fix this? Thanks! ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] Numpy Installation Problem on Redhat Linux
However, I got the following error message: error: Command /usr/bin/g77 -g -Wall -g -Wall -shared build/temp.linux-x86_64-2.6/build/src.linux-x86_64-2.6/scipy/integrate/vodemodule.o build/temp.linux-x86_64-2.6/build/src.linux-x86_64-2.6/fortranobject.o -L/home/username/lib/ -L/usr/lib64 -Lbuild/temp.linux-x86_64-2.6 -lodepack -llinpack_lite -lmach -lblas -lpython2.6 -lg2c -o build/lib.linux-x86_64-2.6/scipy/integrate/vode.so failed with exit status I'm sure there must have been more output? It does say that the command failed, but not _why_ it failed. I suggest posting the entire output either in an email, or on a webpage (gist.github.com, for instance) and giving the link. It's very very hard to debug a build without the build log, so I'd suggest always giving it in the first instance. Paul ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] Numpy Installation Problem on Redhat Linux
Link is a great suggestion! I was hesitating about whether or not to paste such a long output. The site.cfg file is shown in the following link. https://gist.github.com/3059209 The output message for $ python setup.py build --fcompiler=gnu95 can be found at the URL. https://gist.github.com/3059320 Any suggestion is appreciated. On Fri, Jul 6, 2012 at 5:21 AM, Paul Anton Letnes paul.anton.let...@gmail.com wrote: However, I got the following error message: error: Command /usr/bin/g77 -g -Wall -g -Wall -shared build/temp.linux-x86_64-2.6/build/src.linux-x86_64-2.6/scipy/integrate/vodemodule.o build/temp.linux-x86_64-2.6/build/src.linux-x86_64-2.6/fortranobject.o -L/home/username/lib/ -L/usr/lib64 -Lbuild/temp.linux-x86_64-2.6 -lodepack -llinpack_lite -lmach -lblas -lpython2.6 -lg2c -o build/lib.linux-x86_64-2.6/scipy/integrate/vode.so failed with exit status I'm sure there must have been more output? It does say that the command failed, but not _why_ it failed. I suggest posting the entire output either in an email, or on a webpage (gist.github.com, for instance) and giving the link. It's very very hard to debug a build without the build log, so I'd suggest always giving it in the first instance. Paul ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] Numpy Installation Problem on Redhat Linux
I usually find these problems by searching for error in the output, in your case the complete problem is at the bottom of the log. The relocation errors you're seeing are happening because the build process is trying to link in Atlas libraries (located here: /home/hxc249/lib/atlas/lib/) that were not compiled with -fPIC . Are you building ATLAS from source? If so, then you follow the instructions to recompile ATLAS with -fPIC enabled here: http://math-atlas.sourceforge.net/atlas_install/atlas_install.html#SECTION00043000 creating build/temp.linux-x86_64-2.6/numpy/core/blasdot compile options: '-DATLAS_INFO=\3.9.83\ -Inumpy/core/blasdot -I/home/hxc249/lib/atlas/include -Inumpy/core/include -Ibuild/src.linux-x86_64-2.6/numpy/core/include/numpy -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/usr/include/python2.6 -Ibuild/src.linux-x86_64-2.6/numpy/core/src/multiarray -Ibuild/src.linux-x86_64-2.6/numpy/core/src/umath -c' gcc: numpy/core/blasdot/_dotblas.c numpy/core/blasdot/_dotblas.c: In function ‘dotblas_matrixproduct’: numpy/core/blasdot/_dotblas.c:239: warning: comparison of distinct pointer types lacks a cast numpy/core/blasdot/_dotblas.c:257: warning: passing argument 3 of ‘(struct PyObject * (*)(struct PyObject *, struct PyObject *, struct PyArrayObject *))*(PyArray_API + 2240u)’ from incompatible pointer type numpy/core/blasdot/_dotblas.c:257: note: expected ‘struct PyArrayObject *’ but argument is of type ‘struct PyObject *’ numpy/core/blasdot/_dotblas.c:292: warning: passing argument 3 of ‘(struct PyObject * (*)(struct PyObject *, struct PyObject *, struct PyArrayObject *))*(PyArray_API + 2240u)’ from incompatible pointer type numpy/core/blasdot/_dotblas.c:292: note: expected ‘struct PyArrayObject *’ but argument is of type ‘struct PyObject *’ gcc -pthread -shared build/temp.linux-x86_64-2.6/numpy/core/blasdot/_dotblas.o -L/home/hxc249/lib/atlas/lib -L/usr/lib64 -Lbuild/temp.linux-x86_64-2.6 -lptf77blas -lptcblas -latlas -lpython2.6 -o build/lib.linux-x86_64-2.6/numpy/core/_dotblas.so /usr/bin/ld: /home/hxc249/lib/atlas/lib/libptcblas.a(cblas_dptgemm.o): relocation R_X86_64_32 against `.rodata.str1.8' can not be used when making a shared object; recompile with -fPIC /home/hxc249/lib/atlas/lib/libptcblas.a: could not read symbols: Bad value collect2: ld returned 1 exit status /usr/bin/ld: /home/hxc249/lib/atlas/lib/libptcblas.a(cblas_dptgemm.o): relocation R_X86_64_32 against `.rodata.str1.8' can not be used when making a shared object; recompile with -fPIC /home/hxc249/lib/atlas/lib/libptcblas.a: could not read symbols: Bad value collect2: ld returned 1 exit status error: Command gcc -pthread -shared build/temp.linux-x86_64-2.6/numpy/core/blasdot/_dotblas.o -L/home/hxc249/lib/atlas/lib -L/usr/lib64 -Lbuild/temp.linux-x86_64-2.6 -lptf77blas -lptcblas -latlas -lpython2.6 -o build/lib.linux-x86_64-2.6/numpy/core/_dotblas.so failed with exit status 1 On Fri, Jul 6, 2012 at 6:00 AM, Hung-Hsuan Chen hhc...@psu.edu wrote: Link is a great suggestion! I was hesitating about whether or not to paste such a long output. The site.cfg file is shown in the following link. https://gist.github.com/3059209 The output message for $ python setup.py build --fcompiler=gnu95 can be found at the URL. https://gist.github.com/3059320 Any suggestion is appreciated. On Fri, Jul 6, 2012 at 5:21 AM, Paul Anton Letnes paul.anton.let...@gmail.com wrote: However, I got the following error message: error: Command /usr/bin/g77 -g -Wall -g -Wall -shared build/temp.linux-x86_64-2.6/build/src.linux-x86_64-2.6/scipy/integrate/vodemodule.o build/temp.linux-x86_64-2.6/build/src.linux-x86_64-2.6/fortranobject.o -L/home/username/lib/ -L/usr/lib64 -Lbuild/temp.linux-x86_64-2.6 -lodepack -llinpack_lite -lmach -lblas -lpython2.6 -lg2c -o build/lib.linux-x86_64-2.6/scipy/integrate/vode.so failed with exit status I'm sure there must have been more output? It does say that the command failed, but not _why_ it failed. I suggest posting the entire output either in an email, or on a webpage (gist.github.com, for instance) and giving the link. It's very very hard to debug a build without the build log, so I'd suggest always giving it in the first instance. Paul ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] Numpy Installation Problem on Redhat Linux
Thank you. This is very helpful! On Fri, Jul 6, 2012 at 6:23 AM, Aron Ahmadia a...@ahmadia.net wrote: I usually find these problems by searching for error in the output, in your case the complete problem is at the bottom of the log. The relocation errors you're seeing are happening because the build process is trying to link in Atlas libraries (located here: /home/hxc249/lib/atlas/lib/) that were not compiled with -fPIC . Are you building ATLAS from source? If so, then you follow the instructions to recompile ATLAS with -fPIC enabled here: http://math-atlas.sourceforge.net/atlas_install/atlas_install.html#SECTION00043000 creating build/temp.linux-x86_64-2.6/numpy/core/blasdot compile options: '-DATLAS_INFO=\3.9.83\ -Inumpy/core/blasdot -I/home/hxc249/lib/atlas/include -Inumpy/core/include -Ibuild/src.linux-x86_64-2.6/numpy/core/include/numpy -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/usr/include/python2.6 -Ibuild/src.linux-x86_64-2.6/numpy/core/src/multiarray -Ibuild/src.linux-x86_64-2.6/numpy/core/src/umath -c' gcc: numpy/core/blasdot/_dotblas.c numpy/core/blasdot/_dotblas.c: In function ‘dotblas_matrixproduct’: numpy/core/blasdot/_dotblas.c:239: warning: comparison of distinct pointer types lacks a cast numpy/core/blasdot/_dotblas.c:257: warning: passing argument 3 of ‘(struct PyObject * (*)(struct PyObject *, struct PyObject *, struct PyArrayObject *))*(PyArray_API + 2240u)’ from incompatible pointer type numpy/core/blasdot/_dotblas.c:257: note: expected ‘struct PyArrayObject *’ but argument is of type ‘struct PyObject *’ numpy/core/blasdot/_dotblas.c:292: warning: passing argument 3 of ‘(struct PyObject * (*)(struct PyObject *, struct PyObject *, struct PyArrayObject *))*(PyArray_API + 2240u)’ from incompatible pointer type numpy/core/blasdot/_dotblas.c:292: note: expected ‘struct PyArrayObject *’ but argument is of type ‘struct PyObject *’ gcc -pthread -shared build/temp.linux-x86_64-2.6/numpy/core/blasdot/_dotblas.o -L/home/hxc249/lib/atlas/lib -L/usr/lib64 -Lbuild/temp.linux-x86_64-2.6 -lptf77blas -lptcblas -latlas -lpython2.6 -o build/lib.linux-x86_64-2.6/numpy/core/_dotblas.so /usr/bin/ld: /home/hxc249/lib/atlas/lib/libptcblas.a(cblas_dptgemm.o): relocation R_X86_64_32 against `.rodata.str1.8' can not be used when making a shared object; recompile with -fPIC /home/hxc249/lib/atlas/lib/libptcblas.a: could not read symbols: Bad value collect2: ld returned 1 exit status /usr/bin/ld: /home/hxc249/lib/atlas/lib/libptcblas.a(cblas_dptgemm.o): relocation R_X86_64_32 against `.rodata.str1.8' can not be used when making a shared object; recompile with -fPIC /home/hxc249/lib/atlas/lib/libptcblas.a: could not read symbols: Bad value collect2: ld returned 1 exit status error: Command gcc -pthread -shared build/temp.linux-x86_64-2.6/numpy/core/blasdot/_dotblas.o -L/home/hxc249/lib/atlas/lib -L/usr/lib64 -Lbuild/temp.linux-x86_64-2.6 -lptf77blas -lptcblas -latlas -lpython2.6 -o build/lib.linux-x86_64-2.6/numpy/core/_dotblas.so failed with exit status 1 On Fri, Jul 6, 2012 at 6:00 AM, Hung-Hsuan Chen hhc...@psu.edu wrote: Link is a great suggestion! I was hesitating about whether or not to paste such a long output. The site.cfg file is shown in the following link. https://gist.github.com/3059209 The output message for $ python setup.py build --fcompiler=gnu95 can be found at the URL. https://gist.github.com/3059320 Any suggestion is appreciated. On Fri, Jul 6, 2012 at 5:21 AM, Paul Anton Letnes paul.anton.let...@gmail.com wrote: However, I got the following error message: error: Command /usr/bin/g77 -g -Wall -g -Wall -shared build/temp.linux-x86_64-2.6/build/src.linux-x86_64-2.6/scipy/integrate/vodemodule.o build/temp.linux-x86_64-2.6/build/src.linux-x86_64-2.6/fortranobject.o -L/home/username/lib/ -L/usr/lib64 -Lbuild/temp.linux-x86_64-2.6 -lodepack -llinpack_lite -lmach -lblas -lpython2.6 -lg2c -o build/lib.linux-x86_64-2.6/scipy/integrate/vode.so failed with exit status I'm sure there must have been more output? It does say that the command failed, but not _why_ it failed. I suggest posting the entire output either in an email, or on a webpage (gist.github.com, for instance) and giving the link. It's very very hard to debug a build without the build log, so I'd suggest always giving it in the first instance. Paul ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org
[Numpy-discussion] Numpy Installation Problem on Redhat Linux
Dear all, I've built blas, lapack, and atlas libraries, as shown below. $ ls ~/lib/atlas/lib/ libatlas.a libcblas.a libf77blas.a liblapack.a libptcblas.a libptf77blas.a The library location are specified by site.cfg file, as shown below. [DEFAULT] library_dirs = /home/username/lib/atlas/lib include_dirs = /home/username/lib/atlas/include [blas] libraries = libf77blas, libcblas, libatlas [lapack] libraries = liblapack, libf77blas, libcblas, libatlas I've tried to build numpy (version 1.6.2) by $ python setup.py build --fcompiler=gnu However, I got the following error message: error: Command /usr/bin/g77 -g -Wall -g -Wall -shared build/temp.linux-x86_64-2.6/build/src.linux-x86_64-2.6/scipy/integrate/vodemodule.o build/temp.linux-x86_64-2.6/build/src.linux-x86_64-2.6/fortranobject.o -L/home/username/lib/ -L/usr/lib64 -Lbuild/temp.linux-x86_64-2.6 -lodepack -llinpack_lite -lmach -lblas -lpython2.6 -lg2c -o build/lib.linux-x86_64-2.6/scipy/integrate/vode.so failed with exit status I've searched internet for possible solutions whole day but don't have any progress so far. Anyone has any idea of how to fix this? Thanks! ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] Numpy Installation Problem on Redhat Linux
Hi, are you sure that you want g77 and not gfortran? If you want gfortran, you should pass the --fcompiler=gnu95 flag to setup.py. Which redhat version are you building on? (I don't know red hat well enough to comment, but perhaps someone else do...) Paul On 6. juli 2012, at 03:00, Hung-Hsuan Chen wrote: Dear all, I've built blas, lapack, and atlas libraries, as shown below. $ ls ~/lib/atlas/lib/ libatlas.a libcblas.a libf77blas.a liblapack.a libptcblas.a libptf77blas.a The library location are specified by site.cfg file, as shown below. [DEFAULT] library_dirs = /home/username/lib/atlas/lib include_dirs = /home/username/lib/atlas/include [blas] libraries = libf77blas, libcblas, libatlas [lapack] libraries = liblapack, libf77blas, libcblas, libatlas I've tried to build numpy (version 1.6.2) by $ python setup.py build --fcompiler=gnu However, I got the following error message: error: Command /usr/bin/g77 -g -Wall -g -Wall -shared build/temp.linux-x86_64-2.6/build/src.linux-x86_64-2.6/scipy/integrate/vodemodule.o build/temp.linux-x86_64-2.6/build/src.linux-x86_64-2.6/fortranobject.o -L/home/username/lib/ -L/usr/lib64 -Lbuild/temp.linux-x86_64-2.6 -lodepack -llinpack_lite -lmach -lblas -lpython2.6 -lg2c -o build/lib.linux-x86_64-2.6/scipy/integrate/vode.so failed with exit status I've searched internet for possible solutions whole day but don't have any progress so far. Anyone has any idea of how to fix this? Thanks! ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
[Numpy-discussion] numpy installation problem?
Dear list, I am having problems installing matplotlib (from source) and fipy. I had installed numpy from source and it is running well: :~$ python -c import numpy; print numpy.__version__ 1.6.1 After being trying to solve this problem on matplotlib list, I was recommended to ask numpy list. I copy-paste the errors below and forward the mails from matplotlib users. ... creating /usr/local/lib/python2.7/dist-packages/FiPy-2.1.2-py2.7.egg Extracting FiPy-2.1.2-py2.7.egg to /usr/local/lib/python2.7/dist-packages FiPy 2.1.2 is already the active version in easy-install.pth Installed /usr/local/lib/python2.7/dist-packages/FiPy-2.1.2-py2.7.egg Processing dependencies for FiPy==2.1.2 Finished processing dependencies for FiPy==2.1.2 Traceback (most recent call last): File setup.py, line 594, in module __import__(pkg) File /usr/local/lib/python2.7/dist-packages/pysparse-1.2_dev224-py2.7-linux-x86_64.egg/pysparse/__init__.py, line 6, in module from numpy._import_tools import PackageLoader File /usr/local/lib/python2.7/dist-packages/numpy/__init__.py, line 137, in module import add_newdocs File /usr/local/lib/python2.7/dist-packages/numpy/add_newdocs.py, line 9, in module from numpy.lib import add_newdoc File /usr/local/lib/python2.7/dist-packages/numpy/lib/__init__.py, line 13, in module from polynomial import * File /usr/local/lib/python2.7/dist-packages/numpy/lib/polynomial.py, line 11, in module import numpy.core.numeric as NX AttributeError: 'module' object has no attribute 'core' :~/FiPy-2.1.2$ :~/matplotlib$ sudo python setup.py install basedirlist is: ['/usr/local', '/usr'] BUILDING MATPLOTLIB matplotlib: 1.2.x python: 2.7.2+ (default, Oct 4 2011, 20:06:09) [GCC 4.6.1] platform: linux2 REQUIRED DEPENDENCIES numpy: no * You must install numpy 1.4 or later to build * matplotlib. I do not understand why matplotlib can not see numpy. Please, see the forwarded message. My notebook description: Linux 3.0.0-13-generic #22-Ubuntu SMP Wed Nov 2 13:27:26 UTC 2011 x86_64 x86_64 x86_64 GNU/Linux Thank in advance for your help Regards, Lucia ---BeginMessage--- Perhaps you should post that question for the numpy mailing list? Thanks, I will try that. I have no clues Cheers, Lucia On Mon, Mar 5, 2012 at 1:47 PM, ava...@famaf.unc.edu.ar wrote: On Feb 23, 2012 1:39 PM, ava...@famaf.unc.edu.ar wrote: should I reinstall numpy? No need. You should be able to build matplotlib without sudo and then install with sudo python setup.py build sudo python setup.py install Yes! This is how it should be, but it's not. I have gone a litte further trying to solve this. I have found out the following: If I do an import numpy in python run as user, it works. In fact, 'python setup.py build' works perfectly as user. But if I do an import numpy in python run as root, I get the error I pasted in my previous message: :~/matplotlib$ sudo python Python 2.7.2+ (default, Oct 4 2011, 20:06:09) [GCC 4.6.1] on linux2 Type help, copyright, credits or license for more information. import numpy Traceback (most recent call last): File stdin, line 1, in module File /usr/local/lib/python2.7/dist-packages/numpy/__init__.py, line 137, in module import add_newdocs File /usr/local/lib/python2.7/dist-packages/numpy/add_newdocs.py, line 9, in module from numpy.lib import add_newdoc File /usr/local/lib/python2.7/dist-packages/numpy/lib/__init__.py, line 13, in module from polynomial import * File /usr/local/lib/python2.7/dist-packages/numpy/lib/polynomial.py, line 17, in module from numpy.linalg import eigvals, lstsq File /usr/local/lib/python2.7/dist-packages/numpy/linalg/__init__.py, line 48, in module from linalg import * File /usr/local/lib/python2.7/dist-packages/numpy/linalg/linalg.py, line 23, in module from numpy.linalg import lapack_lite ImportError: libifport.so.5: cannot open shared object file: No such file or directory After that I thought it must be something about this libifport.so that numpy uses, but... :~/matplotlib$ locate libifport /opt/intel/Compiler/11.1/038/lib/intel64/libifport.a /opt/intel/Compiler/11.1/038/lib/intel64/libifport.so /opt/intel/Compiler/11.1/038/lib/intel64/libifport.so.5 :~/matplotlib$ :~$ echo $LD_LIBRARY_PATH /opt/intel/Compiler/11.1/038/lib/intel64:/opt/intel/Compiler/11.1/038/mkl/lib/em64t :~$ sudo -s root@:~# echo $LD_LIBRARY_PATH /opt/intel/Compiler/11.1/038/lib/intel64:/opt/intel/Compiler/11.1/038/mkl/lib/em64t So I don't know why python fails to import numpy as root... and I don't know why mpl's installer needs to import numpy to install what has already been built. I haven't been able to solve this issue yet. Thank you all very much for all your help. Cheers, Lucia.
Re: [Numpy-discussion] numpy installation problem?
On Sunday, March 18, 2012, ava...@famaf.unc.edu.ar wrote: Dear list, I am having problems installing matplotlib (from source) and fipy. I had installed numpy from source and it is running well: :~$ python -c import numpy; print numpy.__version__ 1.6.1 After being trying to solve this problem on matplotlib list, I was recommended to ask numpy list. I copy-paste the errors below and forward the mails from matplotlib users. ... creating /usr/local/lib/python2.7/dist-packages/FiPy-2.1.2-py2.7.egg Extracting FiPy-2.1.2-py2.7.egg to /usr/local/lib/python2.7/dist-packages FiPy 2.1.2 is already the active version in easy-install.pth Installed /usr/local/lib/python2.7/dist-packages/FiPy-2.1.2-py2.7.egg Processing dependencies for FiPy==2.1.2 Finished processing dependencies for FiPy==2.1.2 Traceback (most recent call last): File setup.py, line 594, in module __import__(pkg) File /usr/local/lib/python2.7/dist-packages/pysparse-1.2_dev224-py2.7-linux-x86_64.egg/pysparse/__init__.py, line 6, in module from numpy._import_tools import PackageLoader File /usr/local/lib/python2.7/dist-packages/numpy/__init__.py, line 137, in module import add_newdocs File /usr/local/lib/python2.7/dist-packages/numpy/add_newdocs.py, line 9, in module from numpy.lib import add_newdoc File /usr/local/lib/python2.7/dist-packages/numpy/lib/__init__.py, line 13, in module from polynomial import * File /usr/local/lib/python2.7/dist-packages/numpy/lib/polynomial.py, line 11, in module import numpy.core.numeric as NX AttributeError: 'module' object has no attribute 'core' :~/FiPy-2.1.2$ :~/matplotlib$ sudo python setup.py install basedirlist is: ['/usr/local', '/usr'] BUILDING MATPLOTLIB matplotlib: 1.2.x python: 2.7.2+ (default, Oct 4 2011, 20:06:09) [GCC 4.6.1] platform: linux2 REQUIRED DEPENDENCIES numpy: no * You must install numpy 1.4 or later to build * matplotlib. I do not understand why matplotlib can not see numpy. Please, see the forwarded message. My notebook description: Linux 3.0.0-13-generic #22-Ubuntu SMP Wed Nov 2 13:27:26 UTC 2011 x86_64 x86_64 x86_64 GNU/Linux Thank in advance for your help Regards, Lucia Just making sure, where/when did you get your mpl source? There was a bug in mpl master for a while that would not parse numpy's development version number correctly, but it has been fixed since then. Ben Root ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] numpy installation
Waqar Rashid, on 2011-01-02 00:38, wrote: Hi, trying to install numpy on MacOS with python 3.1 Having installation issues. Has anyone managed to install this on the Mac? regards Waqar - you sent this to the IPython-User list, but I think you probably meant to send it to the numpy-discussion list, since your question does not pertain to IPython itself, so I'm forwarding your email there. Also, can you be more specific about what issues you are having? best, -- Paul Ivanov 314 address only used for lists, off-list direct email at: http://pirsquared.org | GPG/PGP key id: 0x0F3E28F7 signature.asc Description: Digital signature ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] numpy installation in ubuntu
thanks, this didn't seem to work. I get a whole range of errors, most importantly SystemError: Cannot compiler 'Python.h'. Perhaps you need to install python-dev|python-devel. Apparently, according to numpy installation guide (herehttp://docs.scipy.org/doc/numpy/user/install.html#fortran-abi-mismatch) i got the wrong compiler installed. How do I find out which 1 I got? 2010/10/19 David da...@silveregg.co.jp On 10/18/2010 10:45 PM, Pauli Virtanen wrote: Mon, 18 Oct 2010 09:07:42 -0400, Ian Goodfellow wrote: To do a standard installation, run sudo python setup.py install from inside the numpy directory Preferably, sudo python setup.py install --prefix=/usr/local and then you don't mess up your package manager. Ubuntu actually does this by default (i.e. the default prefix expands to /usr/local on ubuntu and debian). But I think we should tell people to use the --user for python 2.6 and above by default: that's the safest method, does not require sudo and works on every platform, cheers, David ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] numpy installation in ubuntu
Tue, 19 Oct 2010 21:26:38 +1300, Alex Ter-Sarkissov wrote: thanks, this didn't seem to work. I get a whole range of errors, most importantly SystemError: Cannot compiler 'Python.h'. Perhaps you need to install python-dev|python-devel. I think you should do sudo apt-get install python-dev ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] numpy installation in ubuntu
thanks! it actually worked! maybe u could recommend some good sources/readin on how to install different modules in python run under linux thanks again, alex 2010/10/19 Pauli Virtanen p...@iki.fi Tue, 19 Oct 2010 21:26:38 +1300, Alex Ter-Sarkissov wrote: thanks, this didn't seem to work. I get a whole range of errors, most importantly SystemError: Cannot compiler 'Python.h'. Perhaps you need to install python-dev|python-devel. I think you should do sudo apt-get install python-dev ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
[Numpy-discussion] numpy installation in ubuntu
hi everyone, i'm very new to ubuntu, now trying to install numpy and wxpython. Having unpacked numpy and running the standard commnad in idle from numpy import * i get the message ImportError: Error importing numpy: you should not try to import numpy from its source directory; please exit the numpy source tree, and relaunch your python intepreter from there. I quit the folder with numpy, relaunched python, but the module wasn't even identified. thanks ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] numpy installation in ubuntu
On Mon, Oct 18, 2010 at 11:55 AM, Alex Ter-Sarkissov sigma.z.1...@gmail.com wrote: hi everyone, i'm very new to ubuntu, now trying to install numpy and wxpython. Did you consider installing the Ubuntu provided packages, e.g. via apt-get or the Synaptic Package manager? That is *much* easier - but you won't get the very latest versions. Having unpacked numpy and running the standard commnad in idle Could you clarify what you did? You don't just unpack the archive and use it as it - there is C code that must be compiled etc. Peter ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] numpy installation in ubuntu
To do a standard installation, run sudo python setup.py install from inside the numpy directory Then your import should work elsewhere. By the way, import * can cause difficulties when you're working with several different files. For example, if you have a function called 'save' somewhere that imports something that does 'from numpy import *' you'll have problems because there is a numpy.save. It's better to import numpy with a shorter name, ie, import numpy as N or import numpy as npy than to drop the namespace altogether. On Mon, Oct 18, 2010 at 6:55 AM, Alex Ter-Sarkissov sigma.z.1...@gmail.comwrote: hi everyone, i'm very new to ubuntu, now trying to install numpy and wxpython. Having unpacked numpy and running the standard commnad in idle from numpy import * i get the message ImportError: Error importing numpy: you should not try to import numpy from its source directory; please exit the numpy source tree, and relaunch your python intepreter from there. I quit the folder with numpy, relaunched python, but the module wasn't even identified. thanks ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] numpy installation in ubuntu
Mon, 18 Oct 2010 09:07:42 -0400, Ian Goodfellow wrote: To do a standard installation, run sudo python setup.py install from inside the numpy directory Preferably, sudo python setup.py install --prefix=/usr/local and then you don't mess up your package manager. Pauli ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] numpy installation in ubuntu
On 10/18/2010 10:45 PM, Pauli Virtanen wrote: Mon, 18 Oct 2010 09:07:42 -0400, Ian Goodfellow wrote: To do a standard installation, run sudo python setup.py install from inside the numpy directory Preferably, sudo python setup.py install --prefix=/usr/local and then you don't mess up your package manager. Ubuntu actually does this by default (i.e. the default prefix expands to /usr/local on ubuntu and debian). But I think we should tell people to use the --user for python 2.6 and above by default: that's the safest method, does not require sudo and works on every platform, cheers, David ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] numpy installation problems
2010/8/23 martin djokovic martin.djoko...@gmail.com: /usr/local/lib/python2.4/site-packages/numpy/fft/fftpack_lite.so: undefined symbol: vmldCos2 To me this looks familiar ... I ran into this problem usually when having Python compiled with another compiler than the library. In your case, it's a bit strange, because Python distutils, for compiling numpy, picks up the compiler used for compiling Python. But, obviously, the numpy .so lib loads, just the dependency not. So I think the proposition that you have /two/ Pythons, one which you run as user, and one which you run when installing numpy, looks not like a promising explanation. Can you anyway do the folling: (as normal user)$ which python (as user installing numpy)# which python ? Also you can try if the import numpy runs well when logged in as the user installing numpy. But I believe it doesn't About the Fortran compiler, don't worry. Can you post some snippet of the build process, to see what compiler is issued? (I'm curious because: 1. If it issues an older gcc than that used to compile the .so lib used by the numpy .so lib, 2. this would explain the load error.) Use python setup.py build | tee log-build.txt 21 to get the full log of the build in a log file log-build.txt. Let the 21 alone if you're not on bash, but then the error msg will not be logged probably. Don't be afraid, setup.py build, as the name says, installs nothing, to install one uses setup.py install (which in turn triggers a build). hth, Friedrich ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
[Numpy-discussion] numpy installation problems
Hello everyone, I have an old machine with Fedora 6 installed -numpy was installed but when I tried to install scipy it did not work so I gave up but that messed up my already installed numpy and now I get the following error message import numpy Traceback (most recent call last): File stdin, line 1, in ? File /usr/local/lib/python2.4/site-packages/numpy/__init__.py, line 44, in ? import fft File /usr/local/lib/python2.4/site-packages/numpy/fft/__init__.py, line 4, in ? from fftpack import * File /usr/local/lib/python2.4/site-packages/numpy/fft/fftpack.py, line 28, in ? import fftpack_lite as fftpack ImportError: /usr/local/lib/python2.4/site-packages/numpy/fft/fftpack_lite.so: undefined symbol: vmldCos2 ** I am not very conversant with Linux systems but from googling I am guessing this is to do with the C compiler-sould I reinstall something? Your help would be much appreciated. Thanks ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] numpy installation problems
On Mon, Aug 23, 2010 at 7:29 AM, martin djokovic martin.djoko...@gmail.com wrote: Hello everyone, I have an old machine with Fedora 6 installed -numpy was installed but when I tried to install scipy it did not work so I gave up but that messed up my already installed numpy and now I get the following error message Looks like numpy was built with a special compiler (maybe Intel compiler ?). If so, you need to use the same one to build scipy, cheers, David ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] numpy installation problems
On Sun, Aug 22, 2010 at 5:29 PM, martin djokovic martin.djoko...@gmail.comwrote: Hello everyone, I have an old machine with Fedora 6 installed -numpy was installed but when I tried to install scipy it did not work so I gave up but that messed up my already installed numpy and now I get the following error message import numpy Traceback (most recent call last): File stdin, line 1, in ? File /usr/local/lib/python2.4/site-packages/numpy/__init__.py, line 44, in ? import fft File /usr/local/lib/python2.4/site-packages/numpy/fft/__init__.py, line 4, in ? from fftpack import * File /usr/local/lib/python2.4/site-packages/numpy/fft/fftpack.py, line 28, in ? import fftpack_lite as fftpack ImportError: /usr/local/lib/python2.4/site-packages/numpy/fft/fftpack_lite.so: undefined symbol: vmldCos2 ** I am not very conversant with Linux systems but from googling I am guessing this is to do with the C compiler-sould I reinstall something? Your help would be much appreciated. Thanks Were you trying to install scipy from source or using a package from a repository somewhere? Ben Root ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
[Numpy-discussion] numpy installation problems
Actually I don't need scipy just need to get numpy working again. Scipy I downloaded a tar file from a mirror site. Sorry about the confusion-if I can get numpy working I would be happy. I have tried even installing an older version of numpy suitable for ferdora 6 Thanks a lot ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
[Numpy-discussion] numpy installation problems
Do you think I should reinstall gcc? I do have the root password if nessasary Thanks for the replies ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] numpy installation problems
On 08/23/2010 07:59 AM, martin djokovic wrote: Do you think I should reinstall gcc? You most likely already have gcc, there is no need to reinstall it. The missing symbol refers to the math library from icc, so if you can find the missing libraries, you should be set: 1: get the name of the missing library by running ldd on the .so files which have missing symbols (fftpack_lite.so here). You should get a list of libraries, with some missing. 2: locate the missing libraries on your system. 3: if found, add the path of the libraries into LD_LIBRARY_PATH, e.g. export LD_LIBRARY_PATH=/opt/lib:$LD_LIBRARY_PATH inside your shell 4: if not found, then you may need to reinstall numpy from sources. cheers, David ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] Numpy installation problem
On Jul 24, 2010, at 3:08 PM, Benjamin Root wrote: On Fri, Jul 23, 2010 at 10:10 AM, Jonathan Tu j...@princeton.edu wrote: Hi, I am trying to install Numpy on a Linux cluster running RHEL4. I installed a local copy of Python 2.7 because RHEL4 uses Python 2.3.4 for various internal functionalities. I downloaded the Numpy source code using svn co http://svn.scipy.org/svn/numpy/trunk numpy and then I tried to build using python setup.py build This resulted in the following error: gcc: numpy/linalg/lapack_litemodule.c gcc: numpy/linalg/python_xerbla.c /usr/bin/g77 -g -Wall -g -Wall -shared build/temp.linux-x86_64-2.7/numpy/linalg/lapack_litemodule.o build/temp.linux-x86_64-2.7/numpy/linalg/python_xerbla.o -L/usr/lib64/ATLAS -Lbuild/temp.linux-x86_64-2.7 -llapack -lptf77blas -lptcblas -latlas -lg2c -o build/lib.linux-x86_64-2.7/numpy/linalg/lapack_lite.so /usr/bin/ld: /usr/lib64/ATLAS/liblapack.a(dgeev.o): relocation R_X86_64_32 against `a local symbol' can not be used when making a shared object; recompile with -fPIC /usr/lib64/ATLAS/liblapack.a: could not read symbols: Bad value collect2: ld returned 1 exit status /usr/bin/ld: /usr/lib64/ATLAS/liblapack.a(dgeev.o): relocation R_X86_64_32 against `a local symbol' can not be used when making a shared object; recompile with -fPIC /usr/lib64/ATLAS/liblapack.a: could not read symbols: Bad value collect2: ld returned 1 exit status error: Command /usr/bin/g77 -g -Wall -g -Wall -shared build/temp.linux-x86_64-2.7/numpy/linalg/lapack_litemodule.o build/temp.linux-x86_64-2.7/numpy/linalg/python_xerbla.o -L/usr/lib64/ATLAS -Lbuild/temp.linux-x86_64-2.7 -llapack -lptf77blas -lptcblas -latlas -lg2c -o build/lib.linux-x86_64-2.7/numpy/linalg/lapack_lite.so failed with exit status 1 Full details of the output are attached in stdout.txt and stderr.txt. I thought maybe it was a compiler error so I tried python setup.py build -fcompiler=gnu but this also resulted in errors as well (stdout_2.txt, stderr_2.txt). I just noticed that on both attempts, it is complaining that it can't find a Fortran 90 compiler. I'm not sure if I have the right compiler available. On this cluster I have the following modules: /usr/share/Modules/modulefiles dot module-cvs module-info modules nulluse.own /usr/local/share/Modules/modulefiles mpich/gcc/1.2.7p1/64 openmpi/gcc-ib/1.2.3/64 mpich/intel/1.2.7dmcrp1/64 openmpi/gcc-ib/1.2.5/64 mpich/intel/1.2.7p1/64 openmpi/intel/1.2.3/64 mpich/pgi-7.1/1.2.7p1/64 openmpi/intel-11.0/1.2.8/64 mpich-debug/gcc/1.2.7p1/64 openmpi/intel-9.1/1.2.8/64 mpich-debug/intel/1.2.7p1/64 openmpi/intel-ib/1.1.5/64 mpich-debug/pgi-7.1/1.2.7p1/64 openmpi/intel-ib/1.2.3/64 mvapich/gcc/0.9.9/64 openmpi/intel-ib/1.2.5/64 mvapich/pgi-7.1/0.9.9/64 openmpi/pgi-7.0/1.2.3/64 openmpi/gcc/1.2.8/64 openmpi/pgi-7.1/1.2.5/64 openmpi/gcc/1.3.0/64 openmpi/pgi-7.1/1.2.8/64 openmpi/gcc-ib/1.1.5/64openmpi/pgi-8.0/1.2.8/64 /opt/share/Modules/modulefiles intel/10.0/64/C/10.0.026 intel/9.1/64/default intel/10.0/64/Fortran/10.0.026 intel-mkl/10/64 intel/10.0/64/Iidb/10.0.026intel-mkl/10.1/64 intel/10.0/64/default intel-mkl/9/32 intel/11.1/64/11.1.038 intel-mkl/9/64 intel/11.1/64/11.1.072 pgi/7.0/64 intel/9.1/64/C/9.1.045 pgi/7.1/64 intel/9.1/64/Fortran/9.1.040 pgi/8.0/64 intel/9.1/64/Iidb/9.1.045 If anyone has any ideas, they would be greatly appreciated! I am new to Linux and am unsure how to fix this problem. Jonathan Tu Jonathan, Looking at your error logs, I suspect that the issue is that the ATLAS libraries that were installed on your system were probably built using f90, and then your f77-built objects can't link against ATLAS. Do you have admin access to this machine? If possible, try using the yum package manager to install f90 (its availability depends on whatever RHEL license you have, though...). If you can install f90, I would then remove the numpy build directory and try building it again. I hope this helps, Ben Root ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion Hi Ben, I managed to complete my installation. It required setting up the configure file to reference my local installation of Python, rather than the default /usr/bin/Python. However, I would like to see whether or not I am using the optimized ATLAS/LAPACK
Re: [Numpy-discussion] Numpy installation problem
On Sat 24/07/10 3:39 PM , David Cournapeau courn...@gmail.com wrote: On Sun, Jul 25, 2010 at 4:23 AM, Jonathan Tu wrote: On Jul 24, 2010, at 3:08 PM, Benjamin Root wrote: On Fri, Jul 23, 2010 at 10:10 AM, Jonathan Tu wrote: Hi, I am trying to install Numpy on a Linux cluster running RHEL4. I installed a local copy of Python 2.7 because RHEL4 uses Python 2.3.4 for various internal functionalities. I downloaded the Numpy source code using svn co http://svn.scipy.org/svn/numpy/trunk [1] numpy and then I tried to build using python setup.py build This resulted in the following error: gcc: numpy/linalg/lapack_litemodule.c gcc: numpy/linalg/python_xerbla.c /usr/bin/g77 -g -Wall -g -Wall -shared build/temp.linux-x86_64-2.7/numpy/linalg/lapack_litemodule.o build/temp.linux-x86_64-2.7/numpy/linalg/python_xerbla.o -L/usr/lib64/ATLAS -Lbuild/temp.linux-x86_64-2.7 -llapack -lptf77blas -lptcblas -latlas -lg2c -o build/lib.linux-x86_64-2.7/numpy/linalg/lapack_lite.so /usr/bin/ld: /usr/lib64/ATLAS/liblapack.a(dgeev.o): relocation R_X86_64_32 against `a local symbol' can not be used when making a shared object; recompile with -fPIC /usr/lib64/ATLAS/liblapack.a: could not read symbols: Bad value collect2: ld returned 1 exit status /usr/bin/ld: /usr/lib64/ATLAS/liblapack.a(dgeev.o): relocation R_X86_64_32 against `a local symbol' can not be used when making a shared object; recompile with -fPIC /usr/lib64/ATLAS/liblapack.a: could not read symbols: Bad value collect2: ld returned 1 exit status error: Command /usr/bin/g77 -g -Wall -g -Wall -shared build/temp.linux-x86_64-2.7/numpy/linalg/lapack_litemodule.o build/temp.linux-x86_64-2.7/numpy/linalg/python_xerbla.o -L/usr/lib64/ATLAS -Lbuild/temp.linux-x86_64-2.7 -llapack -lptf77blas -lptcblas -latlas -lg2c -o build/lib.linux-x86_64-2.7/numpy/linalg/lapack_lite.so failed with exit status 1 Full details of the output are attached in stdout.txt and stderr.txt. I thought maybe it was a compiler error so I tried python setup.py build -fcompiler=gnu but this also resulted in errors as well (stdout_2.txt, stderr_2.txt). I just noticed that on both attempts, it is complaining that it can't find a Fortran 90 compiler. I'm not sure if I have the right compiler available. On this cluster I have the following modules: /usr/share/Modules/modulefiles dot module-cvs module-info modules null use.own /usr/local/share/Modules/modulefiles mpich/gcc/1.2.7p1/64 openmpi/gcc-ib/1.2.3/64 mpich/intel/1.2.7dmcrp1/64 openmpi/gcc-ib/1.2.5/64 mpich/intel/1.2.7p1/64 openmpi/intel/1.2.3/64 mpich/pgi-7.1/1.2.7p1/64 openmpi/intel-11.0/1.2.8/64 mpich-debug/gcc/1.2.7p1/64 openmpi/intel-9.1/1.2.8/64 mpich-debug/intel/1.2.7p1/64 openmpi/intel-ib/1.1.5/64 mpich-debug/pgi-7.1/1.2.7p1/64 openmpi/intel-ib/1.2.3/64 mvapich/gcc/0.9.9/64 openmpi/intel-ib/1.2.5/64 mvapich/pgi-7.1/0.9.9/64 openmpi/pgi-7.0/1.2.3/64 openmpi/gcc/1.2.8/64 openmpi/pgi-7.1/1.2.5/64 openmpi/gcc/1.3.0/64 openmpi/pgi-7.1/1.2.8/64 openmpi/gcc-ib/1.1.5/64 openmpi/pgi-8.0/1.2.8/64 /opt/share/Modules/modulefiles intel/10.0/64/C/10.0.026 intel/9.1/64/default intel/10.0/64/Fortran/10.0.026 intel-mkl/10/64 intel/10.0/64/Iidb/10.0.026 intel-mkl/10.1/64 intel/10.0/64/default intel-mkl/9/32 intel/11.1/64/11.1.038 intel-mkl/9/64 intel/11.1/64/11.1.072 pgi/7.0/64 intel/9.1/64/C/9.1.045 pgi/7.1/64 intel/9.1/64/Fortran/9.1.040 pgi/8.0/64 intel/9.1/64/Iidb/9.1.045 If anyone has any ideas, they would be greatly appreciated! I am new to Linux and am unsure how to fix this problem. Jonathan Tu Jonathan, Looking at your error logs, I suspect that the issue is that the ATLAS libraries that were installed on your system were probably built using f90, and then your f77-built objects can't link against ATLAS. Do you have admin access to this machine? If possible, try using the yum package manager to install f90 (its availability depends on whatever RHEL license you have, though...). If you can install f90, I would then remove the numpy build directory and try building it again. I hope this helps, Ben Root ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion [2] Hi Ben, I managed to complete my installation. It required setting up the configure file to reference my local installation of Python, rather than the default /usr/bin/Python. However, I would like to see whether or not I am using the optimized ATLAS/LAPACK libraries for my matrix computations. Run ldd on the concerned extensions:
Re: [Numpy-discussion] Numpy installation problem
On Sun, Jul 25, 2010 at 4:50 AM, Jonathan Tu j...@princeton.edu wrote: I am unable to find the files lapack_lite.so or _dotblas.so. I used the locate command to look for them. If you just installed numpy, locate won't find them as locate uses a database which is usually updated once in a while. Depending on how you installed numpy, you will find lapack_lite.so in /usr, $HOME/.local or somewhere else (and also in the build directory in the numpy source tree). _dotblas.so may not be present, but numpy cannot work without a lapack_lite.so. cheers, David ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] Numpy installation problem
On Jul 24, 2010, at 4:04 PM, Keith Goodman wrote: On Sat, Jul 24, 2010 at 12:58 PM, David Cournapeau courn...@gmail.com wrote: On Sun, Jul 25, 2010 at 4:50 AM, Jonathan Tu j...@princeton.edu wrote: I am unable to find the files lapack_lite.so or _dotblas.so. I used the locate command to look for them. If you just installed numpy, locate won't find them as locate uses a database which is usually updated once in a while. Depending on how you installed numpy, you will find lapack_lite.so in /usr, $HOME/.local or somewhere else (and also in the build directory in the numpy source tree). Here's one way to find where numpy is installed: $ python import numpy numpy module 'numpy' from '/usr/local/lib/python2.6/site-packages/numpy/__init__.pyc' So on my computer numpy is installed in /usr/local/lib/python2.6/site-packages _dotblas.so may not be present, but numpy cannot work without a lapack_lite.so. Thanks for the tip! This worked, and much faster than the manual hunting through directories I'd been trying. Upon running ldd on lapack_lite.so and on _dotblas.so, I got the following (first for lapack_lite, then for _dotblas): libpthread.so.0 = /lib64/tls/libpthread.so.0 (0x002a95792000) libc.so.6 = /lib64/tls/libc.so.6 (0x002a958a7000) /lib64/ld-linux-x86-64.so.2 (0x00552000) libpthread.so.0 = /lib64/tls/libpthread.so.0 (0x002a95d36000) libc.so.6 = /lib64/tls/libc.so.6 (0x002a95e4c000) /lib64/ld-linux-x86-64.so.2 (0x00552000) I am interested in whether my Numpy installation is in fact taking advantage of the LAPACK libraries that are installed on the cluster where I'm running. I know that Numpy can function without such an installation, but I think it is probably faster when taking advantage of optimized libraries. In any case, I know ldd shows library dependencies, but I'm not sure how to make sense of its output, and whether or not it answers my question. Jonathan Tu ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] Numpy installation problem
On Sun, Jul 25, 2010 at 5:11 AM, Jonathan Tu j...@princeton.edu wrote: On Jul 24, 2010, at 4:04 PM, Keith Goodman wrote: On Sat, Jul 24, 2010 at 12:58 PM, David Cournapeau courn...@gmail.com wrote: On Sun, Jul 25, 2010 at 4:50 AM, Jonathan Tu j...@princeton.edu wrote: I am unable to find the files lapack_lite.so or _dotblas.so. I used the locate command to look for them. If you just installed numpy, locate won't find them as locate uses a database which is usually updated once in a while. Depending on how you installed numpy, you will find lapack_lite.so in /usr, $HOME/.local or somewhere else (and also in the build directory in the numpy source tree). Here's one way to find where numpy is installed: $ python import numpy numpy module 'numpy' from '/usr/local/lib/python2.6/site-packages/numpy/__init__.pyc' So on my computer numpy is installed in /usr/local/lib/python2.6/site-packages _dotblas.so may not be present, but numpy cannot work without a lapack_lite.so. Thanks for the tip! This worked, and much faster than the manual hunting through directories I'd been trying. Upon running ldd on lapack_lite.so and on _dotblas.so, I got the following (first for lapack_lite, then for _dotblas): libpthread.so.0 = /lib64/tls/libpthread.so.0 (0x002a95792000) libc.so.6 = /lib64/tls/libc.so.6 (0x002a958a7000) /lib64/ld-linux-x86-64.so.2 (0x00552000) libpthread.so.0 = /lib64/tls/libpthread.so.0 (0x002a95d36000) libc.so.6 = /lib64/tls/libc.so.6 (0x002a95e4c000) /lib64/ld-linux-x86-64.so.2 (0x00552000) I am interested in whether my Numpy installation is in fact taking advantage of the LAPACK libraries that are installed on the cluster where I'm running. I know that Numpy can function without such an installation, but I think it is probably faster when taking advantage of optimized libraries. In any case, I know ldd shows library dependencies, but I'm not sure how to make sense of its output, and whether or not it answers my question. It shows you don't use either atlas or even simple lapack. If your install used atlas, the atlas libraries would show up on those .so with ldd, David ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] Numpy installation problem
On Sun, Jul 25, 2010 at 5:13 AM, David Cournapeau courn...@gmail.com wrote: On Sun, Jul 25, 2010 at 5:11 AM, Jonathan Tu j...@princeton.edu wrote: On Jul 24, 2010, at 4:04 PM, Keith Goodman wrote: On Sat, Jul 24, 2010 at 12:58 PM, David Cournapeau courn...@gmail.com wrote: On Sun, Jul 25, 2010 at 4:50 AM, Jonathan Tu j...@princeton.edu wrote: I am unable to find the files lapack_lite.so or _dotblas.so. I used the locate command to look for them. If you just installed numpy, locate won't find them as locate uses a database which is usually updated once in a while. Depending on how you installed numpy, you will find lapack_lite.so in /usr, $HOME/.local or somewhere else (and also in the build directory in the numpy source tree). Here's one way to find where numpy is installed: $ python import numpy numpy module 'numpy' from '/usr/local/lib/python2.6/site-packages/numpy/__init__.pyc' So on my computer numpy is installed in /usr/local/lib/python2.6/site-packages _dotblas.so may not be present, but numpy cannot work without a lapack_lite.so. Thanks for the tip! This worked, and much faster than the manual hunting through directories I'd been trying. Upon running ldd on lapack_lite.so and on _dotblas.so, I got the following (first for lapack_lite, then for _dotblas): libpthread.so.0 = /lib64/tls/libpthread.so.0 (0x002a95792000) libc.so.6 = /lib64/tls/libc.so.6 (0x002a958a7000) /lib64/ld-linux-x86-64.so.2 (0x00552000) libpthread.so.0 = /lib64/tls/libpthread.so.0 (0x002a95d36000) libc.so.6 = /lib64/tls/libc.so.6 (0x002a95e4c000) /lib64/ld-linux-x86-64.so.2 (0x00552000) I am interested in whether my Numpy installation is in fact taking advantage of the LAPACK libraries that are installed on the cluster where I'm running. I know that Numpy can function without such an installation, but I think it is probably faster when taking advantage of optimized libraries. In any case, I know ldd shows library dependencies, but I'm not sure how to make sense of its output, and whether or not it answers my question. It shows you don't use either atlas or even simple lapack. If your install used atlas, the atlas libraries would show up on those .so with ldd Here is what I would do for RHEL4: - use python 2.6, not 2.7, because the released numpy does not support 2.7 yet. - build atlas 3.8.3 and lapack 3.1.1 by yourself: this is your core issue here. Both lapack and atlas should be built with the -fPIC flag on x86_64 arch (modify the make.inc in lapack to include -fPIC in OPT and NOOPT flags, and add the option -Fa alg -fPIC when calling atlas configure script) David ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] Numpy installation problem
It shows you don't use either atlas or even simple lapack. If your install used atlas, the atlas libraries would show up on those .so with ldd, David Hmm. Ok. What I did for Numpy installation was check out the source code using svn. Then I did python setup.py build where I changed the site.cfg file so that the [Default] category also contains the path to my local Python 2.6.5 installation, which is /home/jhtu/local. Then I did make install and I think there was probably a prefix type option where I specified that I wanted to install it locally. How do I specify that I want to build against ATLAS/LAPACK? I'm certain that they are installed on this cluster. Jonathan Tu ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] Numpy installation problem
On Sun, Jul 25, 2010 at 5:18 AM, Jonathan Tu j...@princeton.edu wrote: It shows you don't use either atlas or even simple lapack. If your install used atlas, the atlas libraries would show up on those .so with ldd, David Hmm. Ok. What I did for Numpy installation was check out the source code using svn. Use a released version instead (1.4.1 is the last one as we speak). Although we try to keep a relatively robust trunk, it does not have the QA put in the releases. Then I did python setup.py build where I changed the site.cfg file so that the [Default] category also contains the path to my local Python 2.6.5 installation, which is /home/jhtu/local. If you install the atlas libraries in /home/jhtu/local/lib, you need something like: [atlas] library_dirs = /home/jhtu/local/lib in your site.cfg Then I did make install and I think there was probably a prefix type option where I specified that I wanted to install it locally. I guess you meant python setup.py install ? there is no makefile in numpy How do I specify that I want to build against ATLAS/LAPACK? I'm certain that they are installed on this cluster. They are, but they are broken, as showed on the logs you posted. The atlas libraries packaged by RHEL 4 (and even 5 IIRC) are hopelessly broken, you need to build atlas by yourself - preferably into an rpm if you want to deploy on a cluster if you have admin rights. David ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] Numpy installation problem
Here is what I would do for RHEL4: - use python 2.6, not 2.7, because the released numpy does not support 2.7 yet. - build atlas 3.8.3 and lapack 3.1.1 by yourself: this is your core issue here. Both lapack and atlas should be built with the -fPIC flag on x86_64 arch (modify the make.inc in lapack to include -fPIC in OPT and NOOPT flags, and add the option -Fa alg -fPIC when calling atlas configure script) David I have built lapack and atlas per your instructions (using http://www.scipy.org/Installing_SciPy/Linux for reference). I think this has been done successfully. My first go at building Numpy was not successful, and I was wondering if perhaps I did a few things wrong. At one point, the website I referenced above suggests that I can make shared libraries by doing cd lib #to where the atlas libraries are make shared # for sequential libraries make ptshared # for threaded libraries I initially did both of these things, which I'm not sure is ok. The above website also says our atlas libraries should now be in the lib subdirectory of the current directory. You should copy them to some-place that you can tell site.cfg about. So I copied the libraries using cp to /home/jhtu/local/lib. The final thing I had to do was modify my site.cfg. I had a few questions about this. First of all, for my default paths, do I need to do library_dirs = /usr/local/bin:/home/jhtu/local/lib or just library_dirs = /home/jhtu/local/lib Finally, to specifiy the lapack libraries, there is a section like [blas_opt] libraries = f77blas,... but also another choice [blas_opt] libraries=ptf77blas,... I think this is related to the make shared vs make ptshared question above, but this is something I know nothing about. I think these are the only things that could be causing my problems. Jonathan Tu___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] Numpy installation problem
On Jul 24, 2010, at 5:46 PM, Jonathan Tu wrote: Here is what I would do for RHEL4: - use python 2.6, not 2.7, because the released numpy does not support 2.7 yet. - build atlas 3.8.3 and lapack 3.1.1 by yourself: this is your core issue here. Both lapack and atlas should be built with the -fPIC flag on x86_64 arch (modify the make.inc in lapack to include -fPIC in OPT and NOOPT flags, and add the option -Fa alg -fPIC when calling atlas configure script) David I have built lapack and atlas per your instructions (using http://www.scipy.org/Installing_SciPy/Linux for reference). I think this has been done successfully. My first go at building Numpy was not successful, and I was wondering if perhaps I did a few things wrong. At one point, the website I referenced above suggests that I can make shared libraries by doing cd lib #to where the atlas libraries are make shared # for sequential libraries make ptshared # for threaded libraries I initially did both of these things, which I'm not sure is ok. The above website also says our atlas libraries should now be in the lib subdirectory of the current directory. You should copy them to some-place that you can tell site.cfg about. So I copied the libraries using cp to /home/jhtu/local/lib. The final thing I had to do was modify my site.cfg. I had a few questions about this. First of all, for my default paths, do I need to do library_dirs = /usr/local/bin:/home/jhtu/local/lib or just library_dirs = /home/jhtu/local/lib Finally, to specifiy the lapack libraries, there is a section like [blas_opt] libraries = f77blas,... but also another choice [blas_opt] libraries=ptf77blas,... I think this is related to the make shared vs make ptshared question above, but this is something I know nothing about. I think these are the only things that could be causing my problems. Also, I recently tried this all again, only doing make shared, and only using the list of libraries without pt. In both cases, when I ran Python interactively and tried to load the numpy module, I got the following: import numpy Traceback (most recent call last): File stdin, line 1, in module File /home/jhtu/local/lib/python2.6/site-packages/numpy/__init__.py, line 132, in module import add_newdocs File /home/jhtu/local/lib/python2.6/site-packages/numpy/add_newdocs.py, line 9, in module from lib import add_newdoc File /home/jhtu/local/lib/python2.6/site-packages/numpy/lib/__init__.py, line 13, in module from polynomial import * File /home/jhtu/local/lib/python2.6/site-packages/numpy/lib/polynomial.py, line 17, in module from numpy.linalg import eigvals, lstsq File /home/jhtu/local/lib/python2.6/site-packages/numpy/linalg/__init__.py, line 47, in module from linalg import * File /home/jhtu/local/lib/python2.6/site-packages/numpy/linalg/linalg.py, line 22, in module from numpy.linalg import lapack_lite ImportError: libptf77blas.so: cannot open shared object file: No such file or directory ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] Numpy installation problem
On Sun, Jul 25, 2010 at 6:50 AM, Jonathan Tu j...@princeton.edu wrote: Also, I recently tried this all again, only doing make shared, and only using the list of libraries without pt. In both cases, when I ran Python interactively and tried to load the numpy module, I got the following: import numpy Traceback (most recent call last): File stdin, line 1, in module File /home/jhtu/local/lib/python2.6/site-packages/numpy/__init__.py, line 132, in module import add_newdocs File /home/jhtu/local/lib/python2.6/site-packages/numpy/add_newdocs.py, line 9, in module from lib import add_newdoc File /home/jhtu/local/lib/python2.6/site-packages/numpy/lib/__init__.py, line 13, in module from polynomial import * File /home/jhtu/local/lib/python2.6/site-packages/numpy/lib/polynomial.py, line 17, in module from numpy.linalg import eigvals, lstsq File /home/jhtu/local/lib/python2.6/site-packages/numpy/linalg/__init__.py, line 47, in module from linalg import * File /home/jhtu/local/lib/python2.6/site-packages/numpy/linalg/linalg.py, line 22, in module from numpy.linalg import lapack_lite ImportError: libptf77blas.so: cannot open shared object file: No such file or directory If you install shared libraries into a directory which is not looked in by default by ld, you should add it to the LD_LIBRARY_PATH, e.g.: LD_LIBRARY_PATH=$HOME/local/lib:$LD_LIBRARY_PATH python -c import numpy David ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] Numpy installation problem
If you install shared libraries into a directory which is not looked
in by default by ld, you should add it to the LD_LIBRARY_PATH, e.g.:
LD_LIBRARY_PATH=$HOME/local/lib:$LD_LIBRARY_PATH python -c import numpy
David
Ok, that makes sense to me. I tried to see what the current value is by doing
echo $LD_LIBRARY_PATH
but it told me that the this is an Undefined variable. That seems strange to
me. I am running on a RHEL4 cluster with a C-shell. I tried to do
setenv LD_LIBRARY_PATH /home/jhtu/local/lib:${LD_LIBRARY_PATH}
and of course got the same error about an undefined variable.
I'm not sure what this means.
___
NumPy-Discussion mailing list
NumPy-Discussion@scipy.org
http://mail.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] Numpy installation problem
On Sun, Jul 25, 2010 at 7:00 AM, Jonathan Tu j...@princeton.edu wrote: If you install shared libraries into a directory which is not looked in by default by ld, you should add it to the LD_LIBRARY_PATH, e.g.: LD_LIBRARY_PATH=$HOME/local/lib:$LD_LIBRARY_PATH python -c import numpy David Ok, that makes sense to me. I tried to see what the current value is by doing echo $LD_LIBRARY_PATH It is very possible that you don't have it defined by default on your platform. The undefined variable may be a peculiarity of the cshell - the instructions I gave you assumed a bourne shell or compatible. David ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] Numpy installation problem
On Jul 24, 2010, at 6:09 PM, David Cournapeau wrote: On Sun, Jul 25, 2010 at 7:00 AM, Jonathan Tu j...@princeton.edu wrote: If you install shared libraries into a directory which is not looked in by default by ld, you should add it to the LD_LIBRARY_PATH, e.g.: LD_LIBRARY_PATH=$HOME/local/lib:$LD_LIBRARY_PATH python -c import numpy David Ok, that makes sense to me. I tried to see what the current value is by doing echo $LD_LIBRARY_PATH It is very possible that you don't have it defined by default on your platform. The undefined variable may be a peculiarity of the cshell - the instructions I gave you assumed a bourne shell or compatible. David Ok, I assumed as much and proceeded by simply setting the environment variable. I did not add the part where you said python -c import numpy What does that part do? It turns out that by fixing my library path, numpy now imports. I assume that my installation of h5py doesn't need to be redone just because I reinstalled Numpy? Jonathan Tu ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] Numpy installation problem
On Sat, Jul 24, 2010 at 3:12 PM, Jonathan Tu j...@princeton.edu wrote: On Jul 24, 2010, at 6:09 PM, David Cournapeau wrote: On Sun, Jul 25, 2010 at 7:00 AM, Jonathan Tu j...@princeton.edu wrote: If you install shared libraries into a directory which is not looked in by default by ld, you should add it to the LD_LIBRARY_PATH, e.g.: LD_LIBRARY_PATH=$HOME/local/lib:$LD_LIBRARY_PATH python -c import numpy David Ok, that makes sense to me. I tried to see what the current value is by doing echo $LD_LIBRARY_PATH It is very possible that you don't have it defined by default on your platform. The undefined variable may be a peculiarity of the cshell - the instructions I gave you assumed a bourne shell or compatible. David Ok, I assumed as much and proceeded by simply setting the environment variable. I did not add the part where you said python -c import numpy What does that part do? It turns out that by fixing my library path, numpy now imports. I assume that my installation of h5py doesn't need to be redone just because I reinstalled Numpy? Try: $ python import h5py.tests h5py.tests.runtests() ... -- Ran 247 tests in 1.180s OK unittest._TextTestResult run=247 errors=0 failures=0 ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] Numpy installation problem
On Sun, Jul 25, 2010 at 7:12 AM, Jonathan Tu j...@princeton.edu wrote: What does that part do? It turns out that by fixing my library path, numpy now imports. I assume that my installation of h5py doesn't need to be redone just because I reinstalled Numpy? Actually, you may have to if you installed h5py against the numpy built from the trunk. I don't think the trunk ABI is forward compatible with 1.4.1, David ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] Numpy installation problem
On Jul 24, 2010, at 6:21 PM, David Cournapeau wrote:
On Sun, Jul 25, 2010 at 7:12 AM, Jonathan Tu j...@princeton.edu wrote:
What does that part do? It turns out that by fixing my library path, numpy
now imports. I assume that my installation of h5py doesn't need to be
redone just because I reinstalled Numpy?
Actually, you may have to if you installed h5py against the numpy
built from the trunk. I don't think the trunk ABI is forward
compatible with 1.4.1,
David
Ok, so I reinstalled numpy as we've discussed, and now I've reinstalled h5py
too. When I test numpy, I get the following
import numpy
numpy.test()
Running unit tests for numpy
Traceback (most recent call last):
File stdin, line 1, in module
File
/home/jhtu/local/lib/python2.6/site-packages/numpy/testing/nosetester.py,
line 326, in test
self._show_system_info()
File
/home/jhtu/local/lib/python2.6/site-packages/numpy/testing/nosetester.py,
line 187, in _show_system_info
nose = import_nose()
File
/home/jhtu/local/lib/python2.6/site-packages/numpy/testing/nosetester.py,
line 69, in import_nose
raise ImportError(msg)
ImportError: Need nose = 0.10.0 for tests - see
http://somethingaboutorange.com/mrl/projects/nose
Note that when I try test(level=1) it tells me this is an unexpected keyword
argument. (The level=1 was suggested by the scipy website.) Though this test
seems to fail, the simple math tests I've tried seem to work ok.
Then I tried to test h5py:
import h5py
import h5py.tests
h5py.tests.runtests()
==
ERROR: test_data (h5py.tests.test_filters.TestFilters)
--
Traceback (most recent call last):
File
/home/jhtu/local/lib/python2.6/site-packages/h5py/tests/test_filters.py, line
124, in test_data
test_dset(s, t, compression=c, shuffle=False)
File
/home/jhtu/local/lib/python2.6/site-packages/h5py/tests/test_filters.py, line
117, in test_dset
dset[...] = arr
File /home/jhtu/local/lib/python2.6/site-packages/h5py/highlevel.py, line
1288, in __setitem__
self.id.write(mspace, fspace, val, mtype)
File h5d.pyx, line 231, in h5py.h5d.DatasetID.write (h5py/h5d.c:2336)
File _proxy.pyx, line 115, in h5py._proxy.dset_rw (h5py/_proxy.c:1143)
TypeError: Not a dataset (Invalid arguments to routine: Inappropriate type)
==
FAIL: (File) Backing store for core driver
--
Traceback (most recent call last):
File
/home/jhtu/local/lib/python2.6/site-packages/h5py/tests/high/test_file.py,
line 135, in test_backing
self.assert_('g' in self.f)
AssertionError
==
FAIL: (File) Append
--
Traceback (most recent call last):
File
/home/jhtu/local/lib/python2.6/site-packages/h5py/tests/high/test_file.py,
line 52, in test_a
self.assert_('g' in self.f)
AssertionError
==
FAIL: (File) Readwrite
--
Traceback (most recent call last):
File
/home/jhtu/local/lib/python2.6/site-packages/h5py/tests/high/test_file.py,
line 72, in test_rp
self.assert_('g' in self.f)
AssertionError
==
FAIL: test_open_close (h5py.tests.test_h5g.TestH5G)
--
Traceback (most recent call last):
File /home/jhtu/local/lib/python2.6/site-packages/h5py/tests/test_h5g.py,
line 39, in test_open_close
self.assert_(self.is_grp(grp))
AssertionError
--
Ran 247 tests in 1.307s
FAILED (failures=4, errors=1)
unittest._TextTestResult run=247 errors=1 failures=4
But again, I seem to be able to open hdf5 files and look into them ok, though
sometimes the files randomly close, i.e.
f = h5py.File( '/path/to/file.h5','r')
...
f
Closed hdf5 file (or something like this)
Should I be worried about these errors, or are things working ok? Someone had
once mentioned to me that the numpy tests are prone to failure.
Jonathan Tu
___
NumPy-Discussion mailing list
NumPy-Discussion@scipy.org
http://mail.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] Numpy installation problem
On Sat, Jul 24, 2010 at 3:39 PM, Jonathan Tu j...@princeton.edu wrote:
On Jul 24, 2010, at 6:21 PM, David Cournapeau wrote:
On Sun, Jul 25, 2010 at 7:12 AM, Jonathan Tu j...@princeton.edu wrote:
What does that part do? It turns out that by fixing my library path, numpy
now imports. I assume that my installation of h5py doesn't need to be
redone just because I reinstalled Numpy?
Actually, you may have to if you installed h5py against the numpy
built from the trunk. I don't think the trunk ABI is forward
compatible with 1.4.1,
David
Ok, so I reinstalled numpy as we've discussed, and now I've reinstalled h5py
too. When I test numpy, I get the following
import numpy
numpy.test()
Running unit tests for numpy
Traceback (most recent call last):
File stdin, line 1, in module
File
/home/jhtu/local/lib/python2.6/site-packages/numpy/testing/nosetester.py,
line 326, in test
self._show_system_info()
File
/home/jhtu/local/lib/python2.6/site-packages/numpy/testing/nosetester.py,
line 187, in _show_system_info
nose = import_nose()
File
/home/jhtu/local/lib/python2.6/site-packages/numpy/testing/nosetester.py,
line 69, in import_nose
raise ImportError(msg)
ImportError: Need nose = 0.10.0 for tests - see
http://somethingaboutorange.com/mrl/projects/nose
Note that when I try test(level=1) it tells me this is an unexpected keyword
argument. (The level=1 was suggested by the scipy website.) Though this
test seems to fail, the simple math tests I've tried seem to work ok.
Then I tried to test h5py:
import h5py
import h5py.tests
h5py.tests.runtests()
==
ERROR: test_data (h5py.tests.test_filters.TestFilters)
--
Traceback (most recent call last):
File
/home/jhtu/local/lib/python2.6/site-packages/h5py/tests/test_filters.py,
line 124, in test_data
test_dset(s, t, compression=c, shuffle=False)
File
/home/jhtu/local/lib/python2.6/site-packages/h5py/tests/test_filters.py,
line 117, in test_dset
dset[...] = arr
File /home/jhtu/local/lib/python2.6/site-packages/h5py/highlevel.py, line
1288, in __setitem__
self.id.write(mspace, fspace, val, mtype)
File h5d.pyx, line 231, in h5py.h5d.DatasetID.write (h5py/h5d.c:2336)
File _proxy.pyx, line 115, in h5py._proxy.dset_rw (h5py/_proxy.c:1143)
TypeError: Not a dataset (Invalid arguments to routine: Inappropriate type)
==
FAIL: (File) Backing store for core driver
--
Traceback (most recent call last):
File
/home/jhtu/local/lib/python2.6/site-packages/h5py/tests/high/test_file.py,
line 135, in test_backing
self.assert_('g' in self.f)
AssertionError
==
FAIL: (File) Append
--
Traceback (most recent call last):
File
/home/jhtu/local/lib/python2.6/site-packages/h5py/tests/high/test_file.py,
line 52, in test_a
self.assert_('g' in self.f)
AssertionError
==
FAIL: (File) Readwrite
--
Traceback (most recent call last):
File
/home/jhtu/local/lib/python2.6/site-packages/h5py/tests/high/test_file.py,
line 72, in test_rp
self.assert_('g' in self.f)
AssertionError
==
FAIL: test_open_close (h5py.tests.test_h5g.TestH5G)
--
Traceback (most recent call last):
File /home/jhtu/local/lib/python2.6/site-packages/h5py/tests/test_h5g.py,
line 39, in test_open_close
self.assert_(self.is_grp(grp))
AssertionError
--
Ran 247 tests in 1.307s
FAILED (failures=4, errors=1)
unittest._TextTestResult run=247 errors=1 failures=4
But again, I seem to be able to open hdf5 files and look into them ok, though
sometimes the files randomly close, i.e.
f = h5py.File( '/path/to/file.h5','r')
...
f
Closed hdf5 file (or something like this)
Should I be worried about these errors, or are things working ok? Someone
had once mentioned to me that the numpy tests are prone to failure.
Yes, you should be worried. To run the numpy tests you need to install
nose. That's what your output said:
ImportError: Need nose = 0.10.0 for tests - see
http://somethingaboutorange.com/mrl/projects/nose
For h5py, you might want to try the h5py list. Did you remove the
build directory? Because I don't know much about installation, I
remove everything: the installed package, the build directory.
Re: [Numpy-discussion] Numpy installation problem
Yes, you should be worried. To run the numpy tests you need to install nose. That's what your output said: ImportError: Need nose = 0.10.0 for tests - see http://somethingaboutorange.com/mrl/projects/nose For h5py, you might want to try the h5py list. Did you remove the build directory? Because I don't know much about installation, I remove everything: the installed package, the build directory. Thanks for the tip on nose. I installed it, and now I see that I have 5 numpy failures: == FAIL: test_lapack (test_build.TestF77Mismatch) -- Traceback (most recent call last): File /home/jhtu/local/lib/python2.6/site-packages/numpy/testing/decorators.py, line 146, in skipper_func return f(*args, **kwargs) File /home/jhtu/local/lib/python2.6/site-packages/numpy/linalg/tests/test_build.py, line 48, in test_lapack information.) AssertionError: Both g77 and gfortran runtimes linked in lapack_lite ! This is likely to cause random crashes and wrong results. See numpy INSTALL.txt for more information. == FAIL: test_cdouble (test_linalg.TestEigh) -- Traceback (most recent call last): File /home/jhtu/local/lib/python2.6/site-packages/numpy/linalg/tests/test_linalg.py, line 221, in test_cdouble self.do(a) File /home/jhtu/local/lib/python2.6/site-packages/numpy/linalg/tests/test_linalg.py, line 259, in do assert_almost_equal(ev, evalues) File /home/jhtu/local/lib/python2.6/site-packages/numpy/linalg/tests/test_linalg.py, line 23, in assert_almost_equal old_assert_almost_equal(a, b, decimal=decimal, **kw) File /home/jhtu/local/lib/python2.6/site-packages/numpy/testing/utils.py, line 437, in assert_almost_equal DESIRED: %s\n % (str(actual), str(desired))) AssertionError: Items are not equal: ACTUAL: [-4.48116078 3.37176039] DESIRED: [-2.60555128+0.j 4.60555128+0.j] == FAIL: test_csingle (test_linalg.TestEigh) -- Traceback (most recent call last): File /home/jhtu/local/lib/python2.6/site-packages/numpy/linalg/tests/test_linalg.py, line 217, in test_csingle self.do(a) File /home/jhtu/local/lib/python2.6/site-packages/numpy/linalg/tests/test_linalg.py, line 259, in do assert_almost_equal(ev, evalues) File /home/jhtu/local/lib/python2.6/site-packages/numpy/linalg/tests/test_linalg.py, line 23, in assert_almost_equal old_assert_almost_equal(a, b, decimal=decimal, **kw) File /home/jhtu/local/lib/python2.6/site-packages/numpy/testing/utils.py, line 437, in assert_almost_equal DESIRED: %s\n % (str(actual), str(desired))) AssertionError: Items are not equal: ACTUAL: [-4.48116064 3.37176037] DESIRED: [-2.60555124+0.j 4.60555124+0.j] == FAIL: test_cdouble (test_linalg.TestEigvalsh) -- Traceback (most recent call last): File /home/jhtu/local/lib/python2.6/site-packages/numpy/linalg/tests/test_linalg.py, line 221, in test_cdouble self.do(a) File /home/jhtu/local/lib/python2.6/site-packages/numpy/linalg/tests/test_linalg.py, line 249, in do assert_almost_equal(ev, evalues) File /home/jhtu/local/lib/python2.6/site-packages/numpy/linalg/tests/test_linalg.py, line 23, in assert_almost_equal old_assert_almost_equal(a, b, decimal=decimal, **kw) File /home/jhtu/local/lib/python2.6/site-packages/numpy/testing/utils.py, line 437, in assert_almost_equal DESIRED: %s\n % (str(actual), str(desired))) AssertionError: Items are not equal: ACTUAL: [-4.48116078+0.j 3.37176039+0.j] DESIRED: [-2.60555128+0.j 4.60555128+0.j] == FAIL: test_csingle (test_linalg.TestEigvalsh) -- Traceback (most recent call last): File /home/jhtu/local/lib/python2.6/site-packages/numpy/linalg/tests/test_linalg.py, line 217, in test_csingle self.do(a) File /home/jhtu/local/lib/python2.6/site-packages/numpy/linalg/tests/test_linalg.py, line 249, in do assert_almost_equal(ev, evalues) File /home/jhtu/local/lib/python2.6/site-packages/numpy/linalg/tests/test_linalg.py, line 23, in assert_almost_equal old_assert_almost_equal(a, b, decimal=decimal, **kw) File /home/jhtu/local/lib/python2.6/site-packages/numpy/testing/utils.py, line 437, in assert_almost_equal DESIRED: %s\n % (str(actual), str(desired))) AssertionError: Items are not equal: ACTUAL: [-4.48116064+0.j 3.37176037+0.j] DESIRED: [-2.60555124+0.j 4.60555124+0.j]
[Numpy-discussion] Numpy installation problem
Hi,I am trying to install Numpy on a Linux cluster running RHEL4. I installed a local copy of Python 2.7 because RHEL4 uses Python 2.3.4 for various internal functionalities. I downloaded the Numpy source code usingsvn co http://svn.scipy.org/svn/numpy/trunk numpyand then I tried to build usingpython setup.py buildThis resulted in the following error:gcc: numpy/linalg/lapack_litemodule.c gcc: numpy/linalg/python_xerbla.c /usr/bin/g77 -g -Wall -g -Wall -shared build/temp.linux-x86_64-2.7/numpy/linalg/lapack_litemodule.o build/temp.linux-x86_64-2.7/numpy/linalg/python_xerbla.o -L/usr/lib64/ATLAS -Lbuild/temp.linux-x86_64-2.7 -llapack -lptf77blas -lptcblas -latlas -lg2c -o build/lib.linux-x86_64-2.7/numpy/linalg/lapack_lite.so /usr/bin/ld: /usr/lib64/ATLAS/liblapack.a(dgeev.o): relocation R_X86_64_32 against `a local symbol' can not be used when making a shared object; recompile with -fPIC /usr/lib64/ATLAS/liblapack.a: could not read symbols: Bad value collect2: ld returned 1 exit status /usr/bin/ld: /usr/lib64/ATLAS/liblapack.a(dgeev.o): relocation R_X86_64_32 against `a local symbol' can not be used when making a shared object; recompile with -fPIC /usr/lib64/ATLAS/liblapack.a: could not read symbols: Bad value collect2: ld returned 1 exit status error: Command "/usr/bin/g77 -g -Wall -g -Wall -shared build/temp.linux-x86_64-2.7/numpy/linalg/lapack_litemodule.o build/temp.linux-x86_64-2.7/numpy/linalg/python_xerbla.o -L/usr/lib64/ATLAS -Lbuild/temp.linux-x86_64-2.7 -llapack -lptf77blas -lptcblas -latlas -lg2c -o build/lib.linux-x86_64-2.7/numpy/linalg/lapack_lite.so" failed with exit status 1Full details of the output are attached in stdout.txt and stderr.txt. I thought maybe it was a compiler error so I triedpython setup.py build -fcompiler=gnubut this also resulted in errors as well (stdout_2.txt, stderr_2.txt).I just noticed that on both attempts, it is complaining that it can't find a Fortran 90 compiler. I'm not sure if I have the right compiler available. On this cluster I have the following modules: /usr/share/Modules/modulefiles dot module-cvs module-info modules nulluse.own /usr/local/share/Modules/modulefiles mpich/gcc/1.2.7p1/64 openmpi/gcc-ib/1.2.3/64mpich/intel/1.2.7dmcrp1/64 openmpi/gcc-ib/1.2.5/64mpich/intel/1.2.7p1/64 openmpi/intel/1.2.3/64mpich/pgi-7.1/1.2.7p1/64openmpi/intel-11.0/1.2.8/64 mpich-debug/gcc/1.2.7p1/64 openmpi/intel-9.1/1.2.8/64 mpich-debug/intel/1.2.7p1/64 openmpi/intel-ib/1.1.5/64 mpich-debug/pgi-7.1/1.2.7p1/64 openmpi/intel-ib/1.2.3/64 mvapich/gcc/0.9.9/64 openmpi/intel-ib/1.2.5/64 mvapich/pgi-7.1/0.9.9/64openmpi/pgi-7.0/1.2.3/64 openmpi/gcc/1.2.8/64 openmpi/pgi-7.1/1.2.5/64 openmpi/gcc/1.3.0/64 openmpi/pgi-7.1/1.2.8/64 openmpi/gcc-ib/1.1.5/64openmpi/pgi-8.0/1.2.8/64 /opt/share/Modules/modulefiles intel/10.0/64/C/10.0.026intel/9.1/64/default intel/10.0/64/Fortran/10.0.026 intel-mkl/10/64intel/10.0/64/Iidb/10.0.026 intel-mkl/10.1/64 intel/10.0/64/default intel-mkl/9/32intel/11.1/64/11.1.038 intel-mkl/9/64intel/11.1/64/11.1.072 pgi/7.0/64 intel/9.1/64/C/9.1.045 pgi/7.1/64 intel/9.1/64/Fortran/9.1.040 pgi/8.0/64 intel/9.1/64/Iidb/9.1.045 If anyone has any ideas, they would be greatly appreciated! I am new to Linux and am unsure how to fix this problem.Jonathan TuRunning from numpy source directory.error: Command /usr/bin/g77 -g -Wall -g -Wall -shared build/temp.linux-x86_64-2.7/numpy/linalg/lapack_litemodule.o build/temp.linux-x86_64-2.7/numpy/linalg/python_xerbla.o -L/usr/lib64/ATLAS -Lbuild/temp.linux-x86_64-2.7 -llapack -lptf77blas -lptcblas -latlas -lg2c -o build/lib.linux-x86_64-2.7/numpy/linalg/lapack_lite.so failed with exit status 1 non-existing path in 'numpy/distutils': 'site.cfg' F2PY Version 2_8512 blas_opt_info: blas_mkl_info: libraries mkl,vml,guide not found in /home/jhtu/local/lib libraries mkl,vml,guide not found in /usr/local/lib64 libraries mkl,vml,guide not found in /usr/local/lib libraries mkl,vml,guide not found in /usr/lib64 libraries mkl,vml,guide not found in /usr/lib NOT AVAILABLE atlas_blas_threads_info: Setting PTATLAS=ATLAS libraries ptf77blas,ptcblas,atlas not found in /home/jhtu/local/lib libraries ptf77blas,ptcblas,atlas not found in /usr/local/lib64 libraries ptf77blas,ptcblas,atlas not found in /usr/local/lib Setting PTATLAS=ATLAS Setting PTATLAS=ATLAS FOUND: libraries = ['ptf77blas', 'ptcblas', 'atlas'] library_dirs = ['/usr/lib64/ATLAS'] language = c include_dirs = ['/usr/include/ATLAS'] customize GnuFCompiler Found executable /usr/bin/g77 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': /*
[Numpy-discussion] numpy installation question (IronPython)
Hello, I simply installed numpy in my Python26 installation, and then copied the numpy directory to my site-packages folder of my IronPython installation. Did I miss any installation steps in doing so? The multiarray module could not be found using IronPython. Thanks. ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] numpy installation question (IronPython)
On Tue, Jul 13, 2010 at 2:20 PM, William Johnston willi...@tenbase2.com wrote: Hello, I simply installed numpy in my Python26 installation, and then copied the numpy directory to my site-packages folder of my IronPython installation. Did I miss any installation steps in doing so? The multiarray module could not be found using IronPython. Hi William, Why do you think that numpy works in IronPython ? I thought most Python modules work only with standard (C) Python Numpy depends heavily on C implementations for most of its functionality. Regards, Sebastian Haase ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] numpy installation question (IronPython)
On Tue, Jul 13, 2010 at 8:26 AM, Sebastian Haase seb.ha...@gmail.com wrote: On Tue, Jul 13, 2010 at 2:20 PM, William Johnston willi...@tenbase2.com wrote: Hello, I simply installed numpy in my Python26 installation, and then copied the numpy directory to my site-packages folder of my IronPython installation. Did I miss any installation steps in doing so? The multiarray module could not be found using IronPython. Hi William, Why do you think that numpy works in IronPython ? I thought most Python modules work only with standard (C) Python Numpy depends heavily on C implementations for most of its functionality. Regards, Sebastian Haase ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion William-- I think you will want to look here to be able to use NumPy in IronPython for the time being: http://code.google.com/p/ironclad/ ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] numpy installation question (IronPython)
On Tue, Jul 13, 2010 at 4:31 AM, Wes McKinney wesmck...@gmail.com wrote: On Tue, Jul 13, 2010 at 8:26 AM, Sebastian Haase seb.ha...@gmail.com wrote: On Tue, Jul 13, 2010 at 2:20 PM, William Johnston willi...@tenbase2.com wrote: Hello, I simply installed numpy in my Python26 installation, and then copied the numpy directory to my site-packages folder of my IronPython installation. Did I miss any installation steps in doing so? The multiarray module could not be found using IronPython. Hi William, Why do you think that numpy works in IronPython ? I thought most Python modules work only with standard (C) Python Numpy depends heavily on C implementations for most of its functionality. Regards, Sebastian Haase ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion William-- I think you will want to look here to be able to use NumPy in IronPython for the time being: http://code.google.com/p/ironclad/ ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion Also, http://www.enthought.com/media/SciPyNumPyDotNet.pdf . SOON right? I've never actually used ironpython (or pypy or, well, anything not cpython). :/ --Josh ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] numpy installation with nonroot python installation
Alright, I solved this by using numscons. On Mon, Mar 23, 2009 at 12:48 AM, charlie charlie.xia@gmail.com wrote: Dear numpyers, I am trying to install numpy 1.3 with my own version of python 2.5. I got stuck with following error: *building 'numpy.core.multiarray' extension compiling C sources C compiler: gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC creating build/temp.linux-x86_64-2.5 creating build/temp.linux-x86_64-2.5/numpy creating build/temp.linux-x86_64-2.5/numpy/core creating build/temp.linux-x86_64-2.5/numpy/core/src compile options: '-Ibuild/src.linux-x86_64-2.5/numpy/core/src -Inumpy/core/include -Ibuild/src.linux-x86_64-2.5/numpy/core/include/numpy -Inumpy/core/src -Inumpy/core/include -I/home/cmb-01/lxia/usr/include/python2.5 -c' gcc: numpy/core/src/multiarraymodule.c gcc -pthread -shared build/temp.linux-x86_64-2.5/numpy/core/src/multiarraymodule.o -L. -lm -lm -lpython2.5 -o build/lib.linux-x86_64-2.5/numpy/core/multiarray.so /usr/bin/ld: cannot find -lpython2.5 collect2: ld returned 1 exit status /usr/bin/ld: cannot find -lpython2.5 collect2: ld returned 1 exit status error: Command gcc -pthread -shared build/temp.linux-x86_64-2.5/numpy/core/src/multiarraymodule.o -L. -lm -lm -lpython2.5 -o build/lib.linux-x86_64-2.5/numpy/core/multiarray.so failed with exit status 1* I guess it is because the ld can find the libpython2.5.so; So i tried following methods: 1. $export LD_LIBRARY_PATH = $HOME/usr/lib # where my libpython2.5.so is in 2. edited the site.cfg file so that: [DEFAULT] library_dirs = ~/usr/lib include_dirs = ~/usr/include search_static_first = false Both methods don't work. But when I remove the -lpython2.5 flags from the compiling command, the command go through without problem. But I don know where to remove this flag in the numpy package. I ran out choice now and thus I want to get help from you. Thanks for any advice. Charlie ___ Numpy-discussion mailing list Numpy-discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] numpy installation as non root using site.cfg
On Fri, Sep 26, 2008 at 18:07, Poul Georg Moses [EMAIL PROTECTED] wrote: Dear mailing list I am trying to install numpy-1.1.1 on a cluster where I do not have root permission. I have succesfully installed \ python2.5.2. I am using the cite.cfg file to include the blas and atlas libraries. I have done that by setting the\ defaults to: library_dirs = /usr/lib include_dirs = /usr/include You need [DEFAULT] library_dirs = /usr/lib include_dirs = /usr/include just like it is in the site.cfg.example -- 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
Re: [Numpy-discussion] numpy installation issues
On Mon, Jul 7, 2008 at 3:11 PM, Chris Bartels [EMAIL PROTECTED] wrote: Hi David (and others) This issue is known: http://www.scipy.org/scipy/numpy/ticket/811 I think this is an issue for the numpy developers. (I don't know how to fix this easily, i can try to install an older version of binutils (if cygwin has these), but this will probably break a lot of other stuff. So that is not my preferred solution.) Well, AFAIK, numpy does not have a single line in assembly, so this looks more like a bug in the cygwin packaging (incompatibilities between gcc and binutiles versions). There is not much we can do about it. cheers, David ___ Numpy-discussion mailing list Numpy-discussion@scipy.org http://projects.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] numpy installation issues
Chris Bartels wrote: Hi, I have been trying to install numpy (as a dependancy of matplotlib) on cygwin. I would like to use the native cygwin-python numpy install, as the cygwin development environment I use is portable on usb disk (http://www.dam.brown.edu/people/sezer/software/cygwin/). (Extremely useful!) It would be even better if i can actually install numpy/scipy/matplotlib on this portable distribution. Unfortunately python setup.py build does give an error. (I installed python with sources, so /usr/lib/python2.5/config is existing. Which seemed to be a problem with another python package when I googled for this error.) It looks like you did not install python correctly. I strongly recommend you to use the python available for cygwin, after having removed the python you installed from sources. Installing the python package does give you /usr/lib/python2.5/config, as can be seen on the cygwin package list. Once you correctly installed the python package from cygwin, remove the build directory in numpy sources, and start again. This should get you further, cheers, David ___ Numpy-discussion mailing list Numpy-discussion@scipy.org http://projects.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] numpy installation issues
Hi David, Thank you for the quick reply. It looks like you did not install python correctly. I strongly recommend you to use the python available for cygwin, after having removed the python you installed from sources. Installing the python package does give you /usr/lib/python2.5/config, as can be seen on the cygwin package list. Sorry, my message was ambiguous: I indeed did this, I installed python from the cygwin installer (in cygwin you can opt to install both binary and sources of a package. Sources are needed, I guess, if you want to compile python modules.) So, I did not compile python myself. Once you correctly installed the python package from cygwin, remove the build directory in numpy sources, and start again. This should get you further, I did this exactly. I even tried with the two different versions of python available in cygwin (2.5.2 and 2.5.1 I believe). Removing the build directory each time. I'm really at a loss here. It apparently does not find the required library, but everything is available in /usr/lib/python ? Kind regards, Chris ___ Numpy-discussion mailing list Numpy-discussion@scipy.org http://projects.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] numpy installation issues
Chris Bartels wrote: Sorry, my message was ambiguous: I indeed did this, I installed python from the cygwin installer Ok. Python sources are not needed to build python extensions. Only the headers and the python runtime are needed. Basically, the problem is that for some reason, the library path flags are not passed to the linker, and I thought this was because of a bad python build (from which numpy build system find those informations). Now, the most likely reason for the problem is that you have LIBPATH/LINKFLAGS in your environment. If so, unset them: they do not work as you would expect with numpy/scipy. cheers, David ___ Numpy-discussion mailing list Numpy-discussion@scipy.org http://projects.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] numpy installation issues
Hi David, Thanks again. Unfortunately these variables are not set in the environment. (I checked with 'env'.) I also reinstalled the cygwin python package (again) and ran 'find . -name libpython* -print', this gives: /usr/bin/libpython2.5.dll /usr/lib/python2.5/config/libpython2.5.dll.a The /usr/lib/python2.5/config/ directory contains the following files: Makefile Setup Setup.config Setup.local config.c config.c.in install-sh libpython2.5.dll.a makesetup python.o But the numpy install is still unable to use these, it gives the same error. Kind regards, Chris On Mon, Jul 7, 2008 at 11:16 AM, David Cournapeau [EMAIL PROTECTED] wrote: Chris Bartels wrote: Sorry, my message was ambiguous: I indeed did this, I installed python from the cygwin installer Ok. Python sources are not needed to build python extensions. Only the headers and the python runtime are needed. Basically, the problem is that for some reason, the library path flags are not passed to the linker, and I thought this was because of a bad python build (from which numpy build system find those informations). Now, the most likely reason for the problem is that you have LIBPATH/LINKFLAGS in your environment. If so, unset them: they do not work as you would expect with numpy/scipy. cheers, David ___ Numpy-discussion mailing list Numpy-discussion@scipy.org http://projects.scipy.org/mailman/listinfo/numpy-discussion ___ Numpy-discussion mailing list Numpy-discussion@scipy.org http://projects.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] numpy installation issues
Chris Bartels wrote: Hi David, Thanks again. Unfortunately these variables are not set in the environment. (I checked with 'env'.) I also reinstalled the cygwin python package (again) and ran 'find . -name libpython* -print', this gives: /usr/bin/libpython2.5.dll /usr/lib/python2.5/config/libpython2.5.dll.a Mmh, ok, I am out of ideas by only looking at your build.log. I don't understand why the linker does not get any LIBPATH information; I will take a look by compiling it by myself, then, cheers, David ___ Numpy-discussion mailing list Numpy-discussion@scipy.org http://projects.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] numpy installation issues
Hi David, I just discovered this: http://mail.python.org/pipermail/python-bugs-list/2006-April/032817.html I'm currently trying. On Mon, Jul 7, 2008 at 2:22 PM, David Cournapeau [EMAIL PROTECTED] wrote: Chris Bartels wrote: Hi David, Thanks again. Unfortunately these variables are not set in the environment. (I checked with 'env'.) I also reinstalled the cygwin python package (again) and ran 'find . -name libpython* -print', this gives: /usr/bin/libpython2.5.dll /usr/lib/python2.5/config/libpython2.5.dll.a Mmh, ok, I am out of ideas by only looking at your build.log. I don't understand why the linker does not get any LIBPATH information; I will take a look by compiling it by myself, then, cheers, David ___ Numpy-discussion mailing list Numpy-discussion@scipy.org http://projects.scipy.org/mailman/listinfo/numpy-discussion ___ Numpy-discussion mailing list Numpy-discussion@scipy.org http://projects.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] numpy installation issues
Hi David (and others) This issue is known: http://www.scipy.org/scipy/numpy/ticket/811 I think this is an issue for the numpy developers. (I don't know how to fix this easily, i can try to install an older version of binutils (if cygwin has these), but this will probably break a lot of other stuff. So that is not my preferred solution.) Kind regards, Chris On Mon, Jul 7, 2008 at 2:55 PM, Chris Bartels [EMAIL PROTECTED] wrote: I created 2 symlinks (libpython2.5.a and libpython2.5.dll.a) in the /usr/lib directory which both point to /usr/lib/python2.5/config/libpython2.5.dll.a This seems to solve the linker problem, now I just get some assembly errors :p Included is a new buildlog, it ends with: gcc: build/src.cygwin-1.5.25-i686-2.5/numpy/core/src/umathmodule.c In file included from numpy/core/src/umathmodule.c.src:2183: numpy/core/src/ufuncobject.c: In function `_extract_pyvals': numpy/core/src/ufuncobject.c:1164: warning: int format, long int arg (arg 4) numpy/core/src/ufuncobject.c:1164: warning: int format, long int arg (arg 5) /tmp/ccWY4IyY.s: Assembler messages: /tmp/ccWY4IyY.s:72160: Error: suffix or operands invalid for `fnstsw' /tmp/ccWY4IyY.s:72415: Error: suffix or operands invalid for `fnstsw' In file included from numpy/core/src/umathmodule.c.src:2183: numpy/core/src/ufuncobject.c: In function `_extract_pyvals': numpy/core/src/ufuncobject.c:1164: warning: int format, long int arg (arg 4) numpy/core/src/ufuncobject.c:1164: warning: int format, long int arg (arg 5) /tmp/ccWY4IyY.s: Assembler messages: /tmp/ccWY4IyY.s:72160: Error: suffix or operands invalid for `fnstsw' /tmp/ccWY4IyY.s:72415: Error: suffix or operands invalid for `fnstsw' error: Command gcc -fno-strict-aliasing -DNDEBUG -g -O3 -Wall -Wstrict-prototypes -Ibuild/src.cygwin-1.5.25-i686-2.5/numpy/core/src -Inumpy/core/include -Ibuild/src.cygwin-1.5.25-i686-2.5/numpy/core -Inumpy/core/src -Inumpy/core/include -I/usr/include/python2.5 -I/usr/include/python2.5 -c build/src.cygwin-1.5.25-i686-2.5/numpy/core/src/umathmodule.c -o build/temp.cygwin-1.5.25-i686-2.5/build/src.cygwin-1.5.25-i686-2.5/numpy/core/src/umathmodule.o failed with exit status 1 Kind regards, Chris On Mon, Jul 7, 2008 at 2:38 PM, Chris Bartels [EMAIL PROTECTED] wrote: Hi David, I just discovered this: http://mail.python.org/pipermail/python-bugs-list/2006-April/032817.html I'm currently trying. On Mon, Jul 7, 2008 at 2:22 PM, David Cournapeau [EMAIL PROTECTED] wrote: Chris Bartels wrote: Hi David, Thanks again. Unfortunately these variables are not set in the environment. (I checked with 'env'.) I also reinstalled the cygwin python package (again) and ran 'find . -name libpython* -print', this gives: /usr/bin/libpython2.5.dll /usr/lib/python2.5/config/libpython2.5.dll.a Mmh, ok, I am out of ideas by only looking at your build.log. I don't understand why the linker does not get any LIBPATH information; I will take a look by compiling it by myself, then, cheers, David ___ Numpy-discussion mailing list Numpy-discussion@scipy.org http://projects.scipy.org/mailman/listinfo/numpy-discussion ___ Numpy-discussion mailing list Numpy-discussion@scipy.org http://projects.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] numpy installation issues
After installing the old binutils. (I hope this will not be necessary for future numpy versions, that these can run on an unmodified cygwin install) I managed to build and install. Running numpy in python now gives some errors in the unit test: Type help, copyright, credits or license for more information. import numpy numpy.test(all=True) Numpy is installed in /usr/lib/python2.5/site-packages/numpy Numpy version 1.1.0 Python version 2.5.1 (r251:54863, May 18 2007, 16:56:43) [GCC 3.4.4 (cygming spe cial, gdc 0.12, using dmd 0.125)] Found 18/18 tests for numpy.core.tests.test_defmatrix Found 3/3 tests for numpy.core.tests.test_errstate Found 3/3 tests for numpy.core.tests.test_memmap Found 286/286 tests for numpy.core.tests.test_multiarray Found 70/70 tests for numpy.core.tests.test_numeric Found 36/36 tests for numpy.core.tests.test_numerictypes Found 12/12 tests for numpy.core.tests.test_records Found 143/143 tests for numpy.core.tests.test_regression Found 7/7 tests for numpy.core.tests.test_scalarmath Found 2/2 tests for numpy.core.tests.test_ufunc Found 16/16 tests for numpy.core.tests.test_umath Found 63/63 tests for numpy.core.tests.test_unicode Found 4/4 tests for numpy.distutils.tests.test_fcompiler_gnu Found 5/5 tests for numpy.distutils.tests.test_misc_util Found 2/2 tests for numpy.fft.tests.test_fftpack Found 3/3 tests for numpy.fft.tests.test_helper Found 10/10 tests for numpy.lib.tests.test_arraysetops Found 1/1 tests for numpy.lib.tests.test_financial Found 53/53 tests for numpy.lib.tests.test_function_base Found 5/5 tests for numpy.lib.tests.test_getlimits Found 6/6 tests for numpy.lib.tests.test_index_tricks Found 15/15 tests for numpy.lib.tests.test_io Found 1/1 tests for numpy.lib.tests.test_machar Found 4/4 tests for numpy.lib.tests.test_polynomial Found 1/1 tests for numpy.lib.tests.test_regression Found 49/49 tests for numpy.lib.tests.test_shape_base Found 15/15 tests for numpy.lib.tests.test_twodim_base Found 43/43 tests for numpy.lib.tests.test_type_check Found 1/1 tests for numpy.lib.tests.test_ufunclike Found 24/24 tests for numpy.lib.tests.test__datasource Found 89/89 tests for numpy.linalg.tests.test_linalg Found 3/3 tests for numpy.linalg.tests.test_regression Found 94/94 tests for numpy.ma.tests.test_core Found 15/15 tests for numpy.ma.tests.test_extras Found 17/17 tests for numpy.ma.tests.test_mrecords Found 36/36 tests for numpy.ma.tests.test_old_ma Found 4/4 tests for numpy.ma.tests.test_subclassing Found 7/7 tests for numpy.tests.test_random Found 16/16 tests for numpy.testing.tests.test_utils Found 5/5 tests for numpy.tests.test_ctypeslib ..E. ... == ERROR: check_basic (numpy.tests.test_ctypeslib.TestLoadLibrary) -- Traceback (most recent call last): File /usr/lib/python2.5/site-packages/numpy/tests/test_ctypeslib.py, line 9, in check_basic np.core.multiarray.__file__) File /usr/lib/python2.5/site-packages/numpy/ctypeslib.py, line 55, in load_l ibrary raise e OSError: No such file or directory -- Ran 1283 tests in 7.533s FAILED (errors=1) unittest._TextTestResult run=1283 errors=1 failures=0 Kind regards, Chris On Mon, Jul 7, 2008 at 3:11 PM, Chris Bartels [EMAIL PROTECTED] wrote: Hi David (and others) This issue is known: http://www.scipy.org/scipy/numpy/ticket/811 I think this is an issue for the numpy developers. (I don't know how to fix this easily, i can try to install an older version of
Re: [Numpy-discussion] Numpy installation
Great !! This works for me. Thanks for your help !! Rgds, Amit On Tue, Apr 1, 2008 at 5:36 PM, Robert Kern [EMAIL PROTECTED] wrote: On Tue, Apr 1, 2008 at 4:21 PM, Amit Itagi [EMAIL PROTECTED] wrote: This directory is just the Python source distribution (post configure and make). I don't have root permissions to our cluster and the default python distribution is an older one. Hence, I have my custom Python distribution in this /Python-2.5.2/ directory. The binary is /Python-2.5.2/python . Okay, don't do that. You will have to actually install Python to another location. For example, make a directory ~/python2.5/. Now go to the Python source directory; it would probably be best to start with a clean one. Configure Python using ~/python2.5 as the prefix: $ ./configure --prefix=~/python2.5 Now make and make install. Add ~/python2.5/bin to your $PATH, preferably before /usr/bin or wherever the old python executable is. Build and install numpy using the ~/python2.5/bin/python binary. You should not need to set the --prefix. -- 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 ___ Numpy-discussion mailing list Numpy-discussion@scipy.org http://projects.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] Numpy installation
On Mon, Mar 31, 2008 at 11:06 PM, Robert Kern [EMAIL PROTECTED] wrote: On Mon, Mar 31, 2008 at 4:17 PM, Amit Itagi [EMAIL PROTECTED] wrote: Hi, I am having problems with numpy installation. 1) These is an atlas 3.8.0 library installed somewhere in the search path. However, the installation gives errors with that installation. Is there a way to tell the installer to install the default (possibly slower) blas, instead of using the one in the path ? Create a site.cfg file with the appropriate section; copy and modify the site.cfg.example file. *I figured how to specify a particular installation of the libraries. I want to do the opposite. How do I specify the following in site.cfg - Don't search for the library. Assume that it is absent and use the default slower library ?* * * 2) Also, my main Python directory is called Python-2.5.2. When I try to configure with the installprefix, it changes Python-2.5.2 to python-2.5.2 and creates a new directory. How can I make the installer not convert the upper-case P to a lower-case ? Can you give more information like the platform you are on, the full path to this directory, the exact commands that you executed, and the results of these commands? *I am installing this on a CENTOS linux platform (64 bit AMD opteron). The path to my python directory is /home/amit/packages/Python-2.5.2 . If I temporarily make the atlas library unavailable (by renaming the directory to some name that is not in the path), I can perform the build. Now in the installation stage, I use python setup.py and then choose the option 2/home/amit/packages/Python-2.5.2. In the proposed sys.argv the path is shown as /home/amit/packages/python-2.5.2. Incidentally, it also creates this new directory during install. * *Thanks Robert. Rgds, Amit* -- 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 ___ Numpy-discussion mailing list Numpy-discussion@scipy.org http://projects.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] Numpy installation
On Tue, Apr 1, 2008 at 8:16 AM, Amit Itagi [EMAIL PROTECTED] wrote: I figured how to specify a particular installation of the libraries. I want to do the opposite. How do I specify the following in site.cfg - Don't search for the library. Assume that it is absent and use the default slower library ? If you want to avoid compiling with say ATLAS, you can do something like ATLAS=None python setup.py build Disabling one specific version of one library is more difficult, though. cheers, David ___ Numpy-discussion mailing list Numpy-discussion@scipy.org http://projects.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] Numpy installation
On Tue, Apr 1, 2008 at 10:16 AM, Amit Itagi [EMAIL PROTECTED] wrote: I am installing this on a CENTOS linux platform (64 bit AMD opteron). The path to my python directory is /home/amit/packages/Python-2.5.2 . If I temporarily make the atlas library unavailable (by renaming the directory to some name that is not in the path), I can perform the build. Now in the installation stage, I use python setup.py and then choose the option 2/home/amit/packages/Python-2.5.2. In the proposed sys.argv the path is shown as /home/amit/packages/python-2.5.2. Incidentally, it also creates this new directory during install. Looking at the code, I can confirm that the menu system is simply buggy and the cause of your problem. Do not use it. -- 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
Re: [Numpy-discussion] Numpy installation
On Tue, Apr 1, 2008 at 10:16 AM, Amit Itagi [EMAIL PROTECTED] wrote: On Mon, Mar 31, 2008 at 11:06 PM, Robert Kern [EMAIL PROTECTED] wrote: On Mon, Mar 31, 2008 at 4:17 PM, Amit Itagi [EMAIL PROTECTED] wrote: Hi, I am having problems with numpy installation. 1) These is an atlas 3.8.0 library installed somewhere in the search path. However, the installation gives errors with that installation. Is there a way to tell the installer to install the default (possibly slower) blas, instead of using the one in the path ? Create a site.cfg file with the appropriate section; copy and modify the site.cfg.example file. I figured how to specify a particular installation of the libraries. I want to do the opposite. How do I specify the following in site.cfg - Don't search for the library. Assume that it is absent and use the default slower library ? There's nothing default about it. You should use the [lapack_opt] section to specify whichever BLAS and LAPACK libraries you like, even if they are not optimized. 2) Also, my main Python directory is called Python-2.5.2. When I try to configure with the installprefix, it changes Python-2.5.2 to python-2.5.2 and creates a new directory. How can I make the installer not convert the upper-case P to a lower-case ? Can you give more information like the platform you are on, the full path to this directory, the exact commands that you executed, and the results of these commands? I am installing this on a CENTOS linux platform (64 bit AMD opteron). The path to my python directory is /home/amit/packages/Python-2.5.2 . If I temporarily make the atlas library unavailable (by renaming the directory to some name that is not in the path), I can perform the build. Now in the installation stage, I use python setup.py and then choose the option 2/home/amit/packages/Python-2.5.2. In the proposed sys.argv the path is shown as /home/amit/packages/python-2.5.2. Incidentally, it also creates this new directory during install. Can you just do a python setup.py install instead of going through the menu system? The menu system may be bitrotten. -- 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
Re: [Numpy-discussion] Numpy installation
On Tue, Apr 1, 2008 at 12:43 PM, David Cournapeau [EMAIL PROTECTED] wrote: On Tue, Apr 1, 2008 at 8:16 AM, Amit Itagi [EMAIL PROTECTED] wrote: I figured how to specify a particular installation of the libraries. I want to do the opposite. How do I specify the following in site.cfg - Don't search for the library. Assume that it is absent and use the default slower library ? If you want to avoid compiling with say ATLAS, you can do something like ATLAS=None python setup.py build *The shell does not understand this command. Is this the correct syntax ? Thanks Rgds, Amit * Disabling one specific version of one library is more difficult, though. cheers, David ___ Numpy-discussion mailing list Numpy-discussion@scipy.org http://projects.scipy.org/mailman/listinfo/numpy-discussion ___ Numpy-discussion mailing list Numpy-discussion@scipy.org http://projects.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] Numpy installation
On Tue, Apr 1, 2008 at 12:43 PM, David Cournapeau [EMAIL PROTECTED] wrote: On Tue, Apr 1, 2008 at 8:16 AM, Amit Itagi [EMAIL PROTECTED] wrote: I figured how to specify a particular installation of the libraries. I want to do the opposite. How do I specify the following in site.cfg - Don't search for the library. Assume that it is absent and use the default slower library ? If you want to avoid compiling with say ATLAS, you can do something like ATLAS=None python setup.py build *Ok, this part works. I am using tcsh. So I had to do setenv ATLAS None. Rgds, Amit * Disabling one specific version of one library is more difficult, though. cheers, David ___ Numpy-discussion mailing list Numpy-discussion@scipy.org http://projects.scipy.org/mailman/listinfo/numpy-discussion ___ Numpy-discussion mailing list Numpy-discussion@scipy.org http://projects.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] Numpy installation
On Tue, Apr 1, 2008 at 1:31 PM, Amit Itagi [EMAIL PROTECTED] wrote: On Tue, Apr 1, 2008 at 1:21 PM, Robert Kern [EMAIL PROTECTED] wrote: On Tue, Apr 1, 2008 at 10:16 AM, Amit Itagi [EMAIL PROTECTED] wrote: I am installing this on a CENTOS linux platform (64 bit AMD opteron). The path to my python directory is /home/amit/packages/Python-2.5.2 . If I temporarily make the atlas library unavailable (by renaming the directory to some name that is not in the path), I can perform the build. Now in the installation stage, I use python setup.py and then choose the option 2/home/amit/packages/Python-2.5.2. In the proposed sys.argv the path is shown as /home/amit/packages/python-2.5.2. Incidentally, it also creates this new directory during install. Looking at the code, I can confirm that the menu system is simply buggy and the cause of your problem. Do not use it. Robert, Could you kindly suggest an alternate way of getting it right ? Just like every other Python package: $ python setup.py build ... $ sudo python setup.py install --prefix=/home/amit/packages/Python-2.5.2 http://docs.python.org/inst/inst.html -- 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
Re: [Numpy-discussion] Numpy installation
Robert, I followed the recommended steps. Now I have numpy and numpy-1.0.4-py2.5.egg-info in Python-2.5.2/lib/python2.5/site-packages. However, I am not able to import numpy at the python prompt. Do I have to set pythonpath or something ? Thanks Rgds, Amit On Tue, Apr 1, 2008 at 2:44 PM, Robert Kern [EMAIL PROTECTED] wrote: On Tue, Apr 1, 2008 at 1:31 PM, Amit Itagi [EMAIL PROTECTED] wrote: On Tue, Apr 1, 2008 at 1:21 PM, Robert Kern [EMAIL PROTECTED] wrote: On Tue, Apr 1, 2008 at 10:16 AM, Amit Itagi [EMAIL PROTECTED] wrote: I am installing this on a CENTOS linux platform (64 bit AMD opteron). The path to my python directory is /home/amit/packages/Python-2.5.2 . If I temporarily make the atlas library unavailable (by renaming the directory to some name that is not in the path), I can perform the build. Now in the installation stage, I use python setup.py and then choose the option 2/home/amit/packages/Python-2.5.2. In the proposed sys.argv the path is shown as /home/amit/packages/python- 2.5.2. Incidentally, it also creates this new directory during install. Looking at the code, I can confirm that the menu system is simply buggy and the cause of your problem. Do not use it. Robert, Could you kindly suggest an alternate way of getting it right ? Just like every other Python package: $ python setup.py build ... $ sudo python setup.py install --prefix=/home/amit/packages/Python-2.5.2 http://docs.python.org/inst/inst.html -- 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 ___ Numpy-discussion mailing list Numpy-discussion@scipy.org http://projects.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] Numpy installation
On Tue, Apr 1, 2008 at 4:03 PM, Amit Itagi [EMAIL PROTECTED] wrote: Robert, I followed the recommended steps. Now I have numpy and numpy-1.0.4-py2.5.egg-info in Python-2.5.2/lib/python2.5/site-packages. However, I am not able to import numpy at the python prompt. Do I have to set pythonpath or something ? Possibly. Exactly what is in this .../Python-2.5.2/ directory? Is the python executable .../Python-2.5.2/bin/python? -- 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
Re: [Numpy-discussion] Numpy installation
On Tue, Apr 1, 2008 at 4:21 PM, Amit Itagi [EMAIL PROTECTED] wrote: This directory is just the Python source distribution (post configure and make). I don't have root permissions to our cluster and the default python distribution is an older one. Hence, I have my custom Python distribution in this /Python-2.5.2/ directory. The binary is /Python-2.5.2/python . Okay, don't do that. You will have to actually install Python to another location. For example, make a directory ~/python2.5/. Now go to the Python source directory; it would probably be best to start with a clean one. Configure Python using ~/python2.5 as the prefix: $ ./configure --prefix=~/python2.5 Now make and make install. Add ~/python2.5/bin to your $PATH, preferably before /usr/bin or wherever the old python executable is. Build and install numpy using the ~/python2.5/bin/python binary. You should not need to set the --prefix. -- 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
[Numpy-discussion] Numpy installation
Hi, I am having problems with numpy installation. 1) These is an atlas 3.8.0 library installed somewhere in the search path. However, the installation gives errors with that installation. Is there a way to tell the installer to install the default (possibly slower) blas, instead of using the one in the path ? 2) Also, my main Python directory is called Python-2.5.2. When I try to configure with the installprefix, it changes Python-2.5.2 to python-2.5.2 and creates a new directory. How can I make the installer not convert the upper-case P to a lower-case ? Thanks Rgds, Amit ___ Numpy-discussion mailing list Numpy-discussion@scipy.org http://projects.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] Numpy installation
On Mon, Mar 31, 2008 at 4:17 PM, Amit Itagi [EMAIL PROTECTED] wrote: Hi, I am having problems with numpy installation. 1) These is an atlas 3.8.0 library installed somewhere in the search path. However, the installation gives errors with that installation. Is there a way to tell the installer to install the default (possibly slower) blas, instead of using the one in the path ? Create a site.cfg file with the appropriate section; copy and modify the site.cfg.example file. 2) Also, my main Python directory is called Python-2.5.2. When I try to configure with the installprefix, it changes Python-2.5.2 to python-2.5.2 and creates a new directory. How can I make the installer not convert the upper-case P to a lower-case ? Can you give more information like the platform you are on, the full path to this directory, the exact commands that you executed, and the results of these commands? -- 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
Re: [Numpy-discussion] numpy installation
Dear sir
while installing numpy i'm getting following errors:
o/p is attached here below.
in that mkl libraries are not found in that path but the thing is that all
mkl libraries are available in the same path!!
so please advice me that what should i do for all these errors!!!
OUTPUT:
Running from numpy source directory.
F2PY Version 2_2522*
blas_opt_info:
blas_mkl_info:
libraries mkl,vml,guide not found in
/home/user17/intel/mkl/10.0.1.014/lib/em64t/
libraries mkl,vml,guide not found in
/home/user17/pulsar/PYTHON-PKG/python/lib
NOT AVAILABLE*
atlas_blas_threads_info:
Setting PTATLAS=ATLAS
Setting PTATLAS=ATLAS
Setting PTATLAS=ATLAS
FOUND:
libraries = ['ptf77blas', 'ptcblas', 'atlas']
library_dirs = ['/home/user17/pulsar/PYTHON-PKG/atlas']
language = c
include_dirs = ['/home/user17/pulsar/PYTHON-PKG/ATLAS/include']
FOUND:
libraries = ['ptf77blas', 'ptcblas', 'atlas']
library_dirs = ['/home/user17/pulsar/PYTHON-PKG/atlas']
language = c
define_macros = [('ATLAS_INFO', '\\?.?.?\\')]
include_dirs = ['/home/user17/pulsar/PYTHON-PKG/ATLAS/include']
lapack_opt_info:
lapack_mkl_info:
mkl_info:
libraries mkl,vml,guide not found in
/home/user17/intel/mkl/10.0.1.014/lib/em64t/
libraries mkl,vml,guide not found in
/home/user17/pulsar/PYTHON-PKG/python/lib
NOT AVAILABLE
NOT AVAILABLE
atlas_threads_info:
Setting PTATLAS=ATLAS
numpy.distutils.system_info.atlas_threads_info
Setting PTATLAS=ATLAS
Setting PTATLAS=ATLAS
FOUND:
libraries = ['lapack', 'ptf77blas', 'ptcblas', 'atlas']
library_dirs = ['/home/user17/pulsar/PYTHON-PKG/atlas']
language = f77
include_dirs = ['/home/user17/pulsar/PYTHON-PKG/ATLAS/include']
FOUND:
libraries = ['lapack', 'ptf77blas', 'ptcblas', 'atlas']
library_dirs = ['/home/user17/pulsar/PYTHON-PKG/atlas']
language = f77
define_macros = [('ATLAS_INFO', '\\?.?.?\\')]
include_dirs = ['/home/user17/pulsar/PYTHON-PKG/ATLAS/include']
running install
running build
running config_fc
running build_src
building py_modules sources
building extension numpy.core.multiarray sources
adding 'build/src.linux-ia64-2.3/numpy/core/config.h' to sources.
adding 'build/src.linux-ia64-2.3/numpy/core/__multiarray_api.h' to
sources.
adding 'build/src.linux-ia64-2.3/numpy/core/src' to include_dirs.
numpy.core - nothing done with h_files=
['build/src.linux-ia64-2.3/numpy/core/src/scalartypes.inc',
'build/src.linux-ia64-2.3/numpy/core/src/arraytypes.inc', 'build/src.linux-
ia64-2.3/numpy/core/config.h', 'build/src.linux-ia64-2.3
/numpy/core/__multiarray_api.h']
building extension numpy.core.umath sources
adding 'build/src.linux-ia64-2.3/numpy/core/config.h' to sources.
adding 'build/src.linux-ia64-2.3/numpy/core/__ufunc_api.h' to sources.
adding 'build/src.linux-ia64-2.3/numpy/core/src' to include_dirs.
numpy.core - nothing done with h_files=
['build/src.linux-ia64-2.3/numpy/core/src/scalartypes.inc',
'build/src.linux-ia64-2.3/numpy/core/src/arraytypes.inc', 'build/src.linux-
ia64-2.3/numpy/core/config.h', 'build/src.linux-ia64-2.3
/numpy/core/__ufunc_api.h']
building extension numpy.core._sort sources
adding 'build/src.linux-ia64-2.3/numpy/core/config.h' to sources.
adding 'build/src.linux-ia64-2.3/numpy/core/__multiarray_api.h' to
sources.
numpy.core - nothing done with h_files=
['build/src.linux-ia64-2.3/numpy/core/config.h',
'build/src.linux-ia64-2.3/numpy/core/__multiarray_api.h']
building extension numpy.core.scalarmath sources
adding 'build/src.linux-ia64-2.3/numpy/core/config.h' to sources.
adding 'build/src.linux-ia64-2.3/numpy/core/__multiarray_api.h' to
sources.
adding 'build/src.linux-ia64-2.3/numpy/core/__ufunc_api.h' to sources.
numpy.core - nothing done with h_files=
['build/src.linux-ia64-2.3/numpy/core/config.h',
'build/src.linux-ia64-2.3/numpy/core/__multiarray_api.h', 'build/src.linux-
ia64-2.3/numpy/core/__ufunc_api.h']
building extension numpy.core._dotblas sources
adding 'numpy/core/blasdot/_dotblas.c' to sources.
building extension numpy.lib._compiled_base sources
building extension numpy.dft.fftpack_lite sources
building extension numpy.linalg.lapack_lite sources
adding 'numpy/linalg/lapack_litemodule.c' to sources.
building extension numpy.random.mtrand sources
Could not locate executable gfortran
Could not locate executable f95
customize GnuFCompiler
customize GnuFCompiler
customize GnuFCompiler using config
gcc options: '-pthread -fno-strict-aliasing -DNDEBUG -g -O3 -Wall
-Wstrict-prototypes -fPIC'
compile options: '-Inumpy/core/src -Inumpy/core/include
-I/home/user17/pulsar/PYTHON-PKG/python/include/python2.3 -c'
gcc: _configtest.c
_configtest.c:7:2: #error No _WIN32
_configtest.c:7:2: #error No _WIN32
failure.
removing: _configtest.c _configtest.o
building data_files sources
running build_py
copying build/src.linux-ia64-2.3/numpy/__config__.py - build/lib.linux-
ia64-2.3/numpy
copying numpy/distutils/system_info.py - build/lib.linux-ia64-2.3
/numpy/distutils
copying
Re: [Numpy-discussion] numpy installation problem
sorry for the silly question: have you done python setup.py install from the numpy src directory, after untarring? then cd out from the src directory and try to import numpy from python. L. On 7/31/07, kingshuk ghosh [EMAIL PROTECTED] wrote: Hi, I downloaded numpy1.0.3-2.tar and unzipped and untared. However somehow new numpy does not work. It invokes the old numpy 0.9.6 when i import numpy from python and type in numpy.version.version . I tried to change path and once I do that and when I do import numpy it says running from source directory and then if I try numpy.version.version it gives some error. Is there something obvious I am missing after unzipping and untaring the numpy source file ? For example do I need to do something to install the new numpy1.0.3 ? Or do I also need to download full python package ? I am trying to run this on Red Hat Linux 3.2.2-5 which has a gcc 3.2.2 and the version of python is 2.4 . Any help will be greatly appreciated. Cheers Kings ___ Numpy-discussion mailing list Numpy-discussion@scipy.org http://projects.scipy.org/mailman/listinfo/numpy-discussion ___ Numpy-discussion mailing list Numpy-discussion@scipy.org http://projects.scipy.org/mailman/listinfo/numpy-discussion
[Numpy-discussion] numpy installation problem
Hi, I downloaded numpy1.0.3-2.tar and unzipped and untared. However somehow new numpy does not work. It invokes the old numpy 0.9.6 when i import numpy from python and type in numpy.version.version . I tried to change path and once I do that and when I do import numpy it says running from source directory and then if I try numpy.version.version it gives some error. Is there something obvious I am missing after unzipping and untaring the numpy source file ? For example do I need to do something to install the new numpy1.0.3 ? Or do I also need to download full python package ? I am trying to run this on Red Hat Linux 3.2.2-5 which has a gcc 3.2.2 and the version of python is 2.4 . Any help will be greatly appreciated. Cheers Kings ___ Numpy-discussion mailing list Numpy-discussion@scipy.org http://projects.scipy.org/mailman/listinfo/numpy-discussion
