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aksharb
Beginner
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mkl library error with scipy and numpy installed

We had working scipy and numpy using mkl on our server machine. we dont know what happened but now scipy.test throws below error.we have /11.0/069 intel cluster toolkit and mkl is included in it.

MKL FATAL ERROR: Cannot load libmkl_lapack.so . os is rhel 5.2 x86_64.

Akshar

The issues: Missing patches, I guess : There are 9 patches for '1.2.7p1'.
( You can read the file mpich-el5.spec, to know the used options, flags.)

# yum install fdupes gdb gcc-gfortran xz
ftp://ftp.pbone.net/mirror/www.pclin...os2010.src.rpm
rpm -Uvh mpich-1.2.7p1-1pclos2010.src.rpm
cd /SOURCE/
xz -d mpich-1.2.7p1.tar.xz

rpmbuild -bb mpich-el5.spec : No errors, the packages are created ..
mpich-1.2.7p1-1.el5.i386.rpm , mpich-devel-1.2.7p1-1.el5.i386.rpm

cd /opt/ && ls -R mpich/ | wc 851 826 : All files are present.
( Please ask, if you want to download the packages, i386 or x86_64.)
EDIT : Sorry, I overlooked that you have x86_64.
..
Attached Files
File Type: txt mpich-el5.spec.txt (8.3 KB, 3 views)

Last edited by knudfl; 10-08-11 at 02:35 AM.
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Old 10-08-11, 03:04 PM #3
aksharb
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Registered: Mar 2011
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thanks for help. Unfortunately i am just user. so cant use yum . i have to install it in my home dir only. what is the solution?
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Old 10-08-11, 07:04 PM #4
knudfl
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OK, may not work without the dependencies. You can of course check with
'rpm -qa | grep ' to know, if they are already installed.

RPM packages are usually created in /home//rpms/* : See post #13 here
http://www.linuxquestions.org/questi...1-a-766486/#13

This package, mpich-1.2.7p1-EL5.x86_64.tar.bz2 is the content of
mpich-1.2.7p1-1.el5.x86_64.rpm + mpich-devel-1.2.7p1-1.el5.x86_64.rpm.

'tar xvf mpich-1.2.7p1-EL5.x86_64.tar.bz2' : And you have all the files.
>> https://docs.google.com/uc?id=0B7S25...nload&hl=en_US

.

Last edited by knudfl; 10-08-11 at 07:06 PM.
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Old 10-16-11, 07:23 PM #5
aksharb
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thanks for the help.
Please let me know how i can use mpich-1.2.7p1-EL5.x86_64.tar.bz2 directly in use? I am normal user and dont have any rights to install/upgarde any rpms.

can you brief on the procedure right from scratch to install the patched/(patches) source.
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Unread Yesterday, 03:49 AM #6
knudfl
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Using the files in the tarball mpich-1.2.7p1-EL5.x86_64.tar.bz2:
Unpack to e.g. /home//opt/mpich/***
Edit mpif90 to your paths. Example "mpif90 command" :
./opt/mpich/ch-p4/bin/mpif90 -

Requirements : The binary f95 must be in your path. Default is /usr/bin/f95
.....


Building mpich-1.2.7p1 manually, patches included :
No libmpichf90.a is created. ( At least I got none a week ago.)


Building rpm packages in /home//rpms/ :
http://www.linuxquestions.org/questi...1-a-766486/#13
rpmbuild -bb mpich-el5.spec :
You can stop the terminal, when the patching has been done,
and continue with a manual './configure' etc. in /rpms/BUILD/mpich-1.2.7p1
....
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6 Replies
Gennady_F_Intel
Moderator
52 Views

Akshar, Please look at this article "Numpy user note". It should help to resolve the issue.
--Gennady
aksharb
Beginner
52 Views

Thanks for the reply. But i have it installed already. Now it is not working. libmkl_lapack.so is present in the path. But it is not getting linked.
python -c 'import scipy;scipy.test();' thorws this error.
can you help me?
52 Views

Did you mean it is also inlcuded in your LD_RUN_PATH or LD_LIBRARY_PATH?

--Vipin

aksharb
Beginner
52 Views

yes it is included in LD_RUN_PATH or LD_LIBRARY_PATH also.
Ying_H_Intel
Employee
52 Views

Hello,

How about link the libmkl_lapack.so explicitly

library_dirs = /opt/intel/composer_xe_2011_sp1.6.233/mkl/lib/ia32
include_dirs = /opt/intel/composer_xe_2011_sp1.6.233/mkl/include
mkl_libs = mkl_intel,mkl_intel_thread,mkl_core
lapack_libs = mkl_lapack95 mkl_lapack

Not sure if it is work as the libmkl_lapack.so was removed in latest mkl for a while. is it possible for you to try the Single interface library libmkl_rt.so from MKL 10.3? as the article

http://software.intel.com/en-us/articles/using-intel-mkl-in-your-python-programs/ and http://software.intel.com/en-us/articles/a-new-linking-model-single-dynamic-library-mkl_rt-since-int...


Here is the compiler and MKL version table

http://software.intel.com/en-us/articles/which-version-of-the-intel-ipp-intel-mkl-and-intel-tbb-libr...

The latest is Intel Composer 12.1.1 and MKL 10.3 update 7.

Best Regards,

Ying H.
aksharb
Beginner
52 Views

Hi,

i have mkl 10.1 with intel cluster toolkit 11 update 069 and os is rhel 5.2