Hi,
I compiled a recent version of AMBER (as of 12/20/2010) using gnu(4.1.2) +
mpich2-1.3.1.
Serial compilation had no problem, but there was a problem with the parallel
version.
Actually, there was no error in the compilation process, but when I tried to
run, I had a problem.
$ gcc -vUsing built-in specs.
Target: x86_64-redhat-linux
Configured with: ../configure --prefix=/usr --mandir=/usr/share/man
--infodir=/usr/share/info --enable-shared --enable-threads=posix
--enable-checking=release --with-system-zlib --enable-__cxa_atexit
--disable-libunwind-exceptions --enable-libgcj-multifile
--enable-languages=c,c++,objc,obj-c++,java,fortran,ada --enable-java-awt=gtk
--disable-dssi --enable-plugin
--with-java-home=/usr/lib/jvm/java-1.4.2-gcj-1.4.2.0/jre --with-cpu=generic
--host=x86_64-redhat-linux
Thread model: posix
gcc version 4.1.2 20080704 (Red Hat 4.1.2-48)
$ cd $AMBERHOME/bin
$ ./mpirun -np 2 ./sander.MPI
APPLICATION TERMINATED WITH THE EXIT STRING: Hangup (signal 1)
$ ./mpirun -np 2 ./pmemd.MPI
APPLICATION TERMINATED WITH THE EXIT STRING: Hangup (signal 1)
No mdout file was created.
However, ptraj.MPI worked fine.
$ ./mpirun -np 2 ./ptraj.MPI
\-/
-/- PTRAJ: a utility for processing trajectory files
/-\
\-/ Version: "AMBER 11.0 integrated" (4/2010)
-/- Executable is: "./ptraj.MPI"
/-\ Running on 2 processor(s)
\-/ MULTIPTRAJ must be run with <TOP> and <INPUT>.
I switched gnu compiler to Intel and then the weird error has gone.
Everything seems to be ok.
Did anybody have a similar experience and know how to solve the problem?
--
Best,
InSuk Joung
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Received on Tue Dec 21 2010 - 11:00:05 PST
