<html>
<head>
<meta content="text/html; charset=windows-1252"
http-equiv="Content-Type">
</head>
<body bgcolor="#FFFFFF" text="#000000">
... wait a minute, I found this on the cluster website
<blockquote>Regardless of which programming environment (compiler
suite) you are using, you should always compile code with the Cray
wrapper commands (<code>cc</code> for C code, <code>CC</code> for
C++ code and <code>ftn</code> for Fortran code). <u>The compiler
wrappers produce statically-linked executables by default; for
dynamic libraries use the </u><u><code>-dynamic</code></u><u>
flag or </u><u><code>export CRAYPE_LINK_TYPE=dynamic</code></u><u>
before building.</u>
Note that dynamic linking is the default when the cudatoolkit
module is loaded. You should include the compiler flags
appropriate to the underlying compiler suite (Intel, GNU, PGI,
Cray). There are also specific options for the <br>
wrappers themselves: see the man pages of <code>ftn</code>, <code>cc</code>,
and <code>CC</code> for details</blockquote>
<code></code> That sounds like what you were saying Satish. I'll try
again with "<code>export CRAYPE_LINK_TYPE=dynamic"</code> and come
back to you! Thanks.<br>
<br>
<br>
<br>
<div class="moz-cite-prefix">On 04/24/2018 04:03 PM, Satish Balay
wrote:<br>
</div>
<blockquote cite="mid:alpine.LFD.2.21.1804240857430.9786@asterix"
type="cite">
<pre wrap="">Ok - I do see: libmkl_intel_lp64.so libmkl_sequential.so libmkl_core.so - these should
be the ones that get picked up.
I do not know why 'cc' is picking up static libraries instead of the
shared ones. Perhaps it needs an extra option
'LDFLAGS=-dynamic'
Satish
On Tue, 24 Apr 2018, Samuel Lanthaler wrote:
</pre>
<blockquote type="cite">
<pre wrap="">Dear Satish,
I get the following when doing the ls:
[lanthale@daint103 mkl]$ ls
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64/
libmkl_ao_worker.so libmkl_blacs_sgimpt_lp64.so
libmkl_intel_lp64.a libmkl_sequential.so
libmkl_avx2.so libmkl_blas95_ilp64.a libmkl_intel_lp64.so
libmkl_tbb_thread.a
libmkl_avx512_mic.so libmkl_blas95_lp64.a libmkl_intel_thread.a
libmkl_tbb_thread.so
libmkl_avx512.so libmkl_cdft_core.a libmkl_intel_thread.so
libmkl_vml_avx2.so
libmkl_avx.so libmkl_cdft_core.so libmkl_lapack95_ilp64.a
libmkl_vml_avx512_mic.so
libmkl_blacs_intelmpi_ilp64.a libmkl_core.a libmkl_lapack95_lp64.a
libmkl_vml_avx512.so
libmkl_blacs_intelmpi_ilp64.so libmkl_core.so libmkl_mc3.so
libmkl_vml_avx.so
libmkl_blacs_intelmpi_lp64.a libmkl_def.so libmkl_mc.so
libmkl_vml_cmpt.so
libmkl_blacs_intelmpi_lp64.so libmkl_gf_ilp64.a libmkl_pgi_thread.a
libmkl_vml_def.so
libmkl_blacs_openmpi_ilp64.a libmkl_gf_ilp64.so libmkl_pgi_thread.so
libmkl_vml_mc2.so
libmkl_blacs_openmpi_ilp64.so libmkl_gf_lp64.a libmkl_rt.so
libmkl_vml_mc3.so
libmkl_blacs_openmpi_lp64.a libmkl_gf_lp64.so libmkl_scalapack_ilp64.a
libmkl_vml_mc.so
libmkl_blacs_openmpi_lp64.so libmkl_gnu_thread.a libmkl_scalapack_ilp64.so
locale
libmkl_blacs_sgimpt_ilp64.a libmkl_gnu_thread.so libmkl_scalapack_lp64.a
libmkl_blacs_sgimpt_ilp64.so libmkl_intel_ilp64.a libmkl_scalapack_lp64.so
libmkl_blacs_sgimpt_lp64.a libmkl_intel_ilp64.so libmkl_sequential.a
Cheers,
Samuel
On 04/24/2018 03:50 PM, Satish Balay wrote:
</pre>
<blockquote type="cite">
<pre wrap="">Executing: cc -o /tmp/petsc-tyd_Hm/config.libraries/conftest -O
/tmp/petsc-tyd_Hm/config.libraries/conftest.o
-Wl,-rpath,/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64
-L/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64
-lmkl_intel_lp64 -lmkl_sequential -lmkl_core -lpthread -lstdc++ -ldl
Possible ERROR while running linker: exit code 256
stderr:
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64/libmkl_core.a(mkl_semaphore.o):
In function `mkl_serv_load_inspector':
mkl_semaphore.c:(.text+0x123): warning: Using 'dlopen' in statically linked
applications requires at runtime the shared libraries from the glibc version
used for linking
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64/libmkl_core.a(dgetrs.o):
In function `mkl_lapack_dgetrs':
dgetrs_gen.f:(.text+0x224): undefined reference to `mkl_blas_dtrsm'
dgetrs_gen.f:(.text+0x2b1): undefined reference to `mkl_blas_dtrsm'
dgetrs_gen.f:(.text+0x2e7): undefined reference to `mkl_lapack_dlaswp'
<<<<<<<<
For some reason the compiler is picking up static version of MKL - instead
of shared libraries.
What do you have for:
ls /opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64/
Satish
On Tue, 24 Apr 2018, Samuel Lanthaler wrote:
</pre>
<blockquote type="cite">
<pre wrap="">Dear Satish and Stefano,
Thank you for your answers. I believe I had initially tried to use the
option
--with-blaslapack-dir=[...], instead of specifying lib and include
directly.
But that gives me an error message:
*******************************************************************************
UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for
details):
-------------------------------------------------------------------------------
You set a value for --with-blaslapack-dir=<dir>, but
/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl cannot be used
*******************************************************************************
I attach the new configure.log. Do you think there is something wrong with
the
mkl version that I'm trying to use? Or is it only related to petsc?
Cheers,
Samuel
On 04/24/2018 02:55 PM, Satish Balay wrote:
</pre>
<blockquote type="cite">
<pre wrap="">On Tue, 24 Apr 2018, Samuel Lanthaler wrote:
</pre>
<blockquote type="cite">
<pre wrap="">Hi there,
I was wondering if you could help me with the correct configuration of
PETSc-dev version on a cluster (<a class="moz-txt-link-freetext" href="https://www.cscs.ch/">https://www.cscs.ch/</a>)? I'm not sure which
information would be useful to you, but basically the problem seems to be
in
correctly compiling it with intel compiler and the existing mkl library.
The pre-installed mkl version is
intel/17.0.4.196
I have tried various things and finally, I got it at least to compile
with
the
following options (options chosen in reference to the mkl link
advisor...):
./configure --with-fc=ftn --with-cc=cc --with-cxx=CC --with-debugging=0
--with-scalar-type=complex --download-scalapack --download-mumps=yes
--download-superlu --with-batch --known-mpi-shared-libraries=1
*--with-blaslapack-lib=*" ${MKLROOT}/lib/intel64/libmkl_blas95_lp64.a
${MKLROOT}/lib/intel64/libmkl_lapack95_lp64.a -Wl,--start-group
${MKLROOT}/lib/intel64/libmkl_intel_lp64.a
${MKLROOT}/lib/intel64/libmkl_sequential.a
${MKLROOT}/lib/intel64/libmkl_core.a -Wl,--end-group -lpthread -lm -ldl"
*--with-blaslapack-include*="[/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/include,/opt/intel/compilers_and_libraries_2017.4.196/linux/mkl/include/intel64/lp64]"
</pre>
</blockquote>
<pre wrap="">Can you remove the above 2 options [--with-blaslapack-lib,
--with-blaslapack-include] and use:
--with-blas-lapack-dir=${MKLROOT}
And see if you still have this problem?
Satish
</pre>
<blockquote type="cite">
<pre wrap="">--known-64-bit-blas-indices=0
After compilation, when trying to compile
/users/lanthale/petsc-git/src/snes/examples/tutorials/ex5f I get linking
errors (attached). Would anyone be able to help me out here? I really
don't
have a good understanding of this.
I'm attaching the configuration.log file, as well as the linking errors
when
trying to compile ex5f.
Thank you very much in advance!
Best regards,
Samuel
</pre>
</blockquote>
</blockquote>
<pre wrap="">
</pre>
</blockquote>
</blockquote>
<pre wrap="">
</pre>
</blockquote>
<pre wrap="">
</pre>
</blockquote>
<br>
</body>
</html>