Re: AMBER: test of parallel sander 10 fail

From: Thomas Cheatham III <>
Date: Tue, 15 Jul 2008 11:41:12 -0600 (Mountain Standard Time)

> I tried to compile AMBER 10 for my own use (without root) using the intel
> ifort compiler and mpich2. Everything went smoothly until running the tests
> for the parallel comilation (see error below). First, I compiled mpich2 using
> the intel compilers (icc and ifort) in a directory /<dir>/mpich2-1.0.7. All
> tthe tests from the mpich2 installation guide worked fine. Then I compiled
> AMBER 10 first serial and then parallel (with $MPI_HOME set to
> /<dir>/mpich2-1.0.7). I set $DO_PARALLEL to "mpirun -n 4" or "mpiexec -n 4" or
> "mpiexec -np 4". Always I get same error when "make test.parallel.MM <
> Fatal error in MPI_Comm_rank: Invalid communicator, error stack:
> MPI_Comm_rank(107): MPI_Comm_rank(comm=0x0, rank=0x14150f0) failed

I had errors similar to this just yesterday and realized I was running the
wrong mpirun script (due to vagaries of the system setup on the machine I
was using that use modules and various generic wrappers). If you have
multiple MPI versions, make sure you are using the mpich2-1.0.7 mpi setup
commands and not some other...

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
Received on Wed Jul 16 2008 - 06:07:39 PDT
Custom Search