Re: NAMD compilation / TACC Ranger

From: Axel Kohlmeyer (
Date: Thu Aug 28 2008 - 14:12:36 CDT

On Thu, 28 Aug 2008, Arturas Ziemys wrote:

AZ> Hi,
AZ> I'm trying to compile NAMD 2.6 on Ranger. I got some advices how to do
AZ> modifying environment and using proper compilers and libs. charm++ and NAMD
AZ> compiles with warnings. When NAMD is started it reads input, but fails about
AZ> libraries or environment. I understand that this list is not probably the
AZ> best place to discuss the peculiarities of TACC/Ranger, but I hope that I
AZ> could get some valuable advices or insights, while I'm waiting help from
AZ> Ranger staff.


please look closer. you have a segmentation fault.
that could originate in incompatible libraries, but
could also mean that your input is not correct or
files are not accessable. you are using an MPICH based
MPI implementation and they tend to drop the last lines
of output when a job crashes. try running your input
with a standalone version and make sure it is working

AZ> I try to compile using intel 10.1 compiler with fftw2.2.5 and mvapich. I do
AZ> attach my log file. I modify my environment with :

some early intel 10.1 compiler patchlevel have serious problems
with certain (scientific) codes. you may want to try compiling
with gcc/g++ to make sure that it is not that compiler that is
at fault...


AZ> module unload mvapich2
AZ> module unload mvapich
AZ> module swap pgi intel
AZ> module load mvapich
AZ> Best
AZ> Arturas

Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.

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