AMBER Archive (2007)

Subject: RE: AMBER: sander MPI fails included tests

From: Sergio Wong (swong_at_mccammon.ucsd.edu)
Date: Tue Jun 26 2007 - 15:58:04 CDT

HI;

>> # Generated via command: ./configure -mpich -static ifort_x86_64
>>> What did you have DO_PARALLEL set to?
>
> I am pretty sure this is a compiler issue. Can you check what version of the
> intel compiler you are using (ifort -V). I have just built this on my system
> - Intel EM64T (Pentium-D) on RHEL 4.0 with ifort v9.1.039 and it passes all
> tests in both serial and 2 processor MPI (mpich2 v1.0.3) .

This is my set up:

Intel(R) Fortran Compiler for Intel(R) EM64T-based applications, Version
9.1 Build 20060323 Package ID: l_fc_p_9.1.032

mpich version 1.2.7
MPICH configure: --with-device=ch_gm --enable-sharedlib
-prefix=/opt/mpich/myrinet/intel -opt=-O2 -c++=icpc
-lib=-Wl,-rpath,/opt/gm/lib64/ -L/opt/gm/lib64/ -lgm -lpthread

> Please first check that you have applied bugfix.all from
> http://amber.scripps.edu/bugfixes90.html and make clean / make parallel.

Yes, these were applied from the beginning.

If
> this still fails then see if you can download a newer version of the
> Intel compiler from Intel's site. This should hopefully fix the problem.

OK, so the current version on the Intel site is 10. I downloaded that
compiler (ifort) and tried the installation without linking to the MKL
library.
The same error occurs along with some new messages:

forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image PC Routine Line Source
sander.MPI 00000000005466D5 Unknown Unknown
Unknown
sander.MPI 0000000000514727 Unknown Unknown
Unknown
sander.MPI 00000000006F3C45 Unknown Unknown
Unknown
sander.MPI 00000000004F5B27 Unknown Unknown
Unknown
sander.MPI 00000000004BFD5C Unknown Unknown
Unknown
sander.MPI 00000000004B5605 Unknown Unknown
Unknown
sander.MPI 0000000000408962 Unknown Unknown
Unknown
libc.so.6 0000003D2051C3FB Unknown Unknown
Unknown
sander.MPI 00000000004088AA Unknown Unknown
Unknown

In this latter compilation, I did not use the -static flag. So updating
the compiler didn't work. I get the same error(s) for sander.MPI
regardless of the compiler or usage of the MKL libraries.

Interestingly; using the new compiler (version
10) and the old MKL libraries (version 8.1), I was able to compile and
test pmemd successfully. Pmemd passes all the tests. This is true
whether I use the MKL libraries or not.

The new compiler info is:
Intel(R) Fortran Compiler for applications running on Intel(R) 64, Version
10.0 Build 20070426 Package ID: l_fc_p_10.0.023

Thanks

-Sergio
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