[AMBER-Developers] AmberTools17, intel, -mkl vs setting MKL_HOME

From: David Case <david.case.rutgers.edu>
Date: Fri, 31 Mar 2017 11:24:43 -0400

Hoping someone might recognize this symptom, and know what to do:

Using Intel compilers (any recent version) there is a difference in
AmberTools between passing the "-mkl" flag to configure, and setting
the MKL_HOME environment variable. The former option is relatively new,
whereas the latter is what we have used for some time.

As Scott and others have found, using "-mkl" breaks the sanderapi:
python cannot find mkl_serv_getenv, which is in lib_mkl_core.so
libraries, which are apparently not getting properly linked in to

If one instead sets MKL_HOME, things work fine, presumably because
configure2 creates a config.h file that explicitly links to libmkl_core.a.
I've tried adding -lmkl_core to the config.h file created by configure2,
but without success.

Minor point: using -mkl rather than setting MKL_HOME leads to roundoff
differences in many of the sqm tests. But users of the intel compilers
can probably recognize these for what they are.

If anyone can figure out how to get the pysander API to find mkl_serv_getenv
when the -mkl flag is set, that would be a big help.


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Received on Fri Mar 31 2017 - 08:30:03 PDT
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