[AMBER-Developers] ptraj.MPI in amber12

From: Jodi Ann Hadden <jodih.uga.edu>
Date: Wed, 2 May 2012 19:15:50 +0000

I am noticing that ptraj.MPI is not being generated by the default build protocol for AMBER12 on any of the machines I've compiled it on. These are either fully patched versions of AMBER12 or recent git pulls. Any suggestions?

Two examples machine configurations are:

RHEL6 server, gnu 4.4.6, mvapich2 1.4.1p1
RHEL5, gnu 4.4.6, openMPI 1.4.2

I'm just doing what I though was the standard procedure now:

./configure gnu
make -j4 install
make test
./configure -mpi gnu
make -j4 install
make test

Everything appears to compile fine, all the tests pass, everything seems normal and in working order, but ptraj.MPI is missing. Is there a command I can use to try to build it individually? I tried going down into $AMBERHOME/AmberTools/src/ptraj and doing a make clean/make, but got an error about a missing file:

[installer.tolkien ptraj]$ make
cd pdb && make
make[1]: Entering directory `/programs/gpu/mmpbsa_test/amber12/AmberTools/src/ptraj/pdb'
mpicc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DMPI -c -o pdbrun.o pdbrun.c
mpicc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DMPI -c -o pdb_read.o pdb_read.c
mpicc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DMPI -c -o pdb_sprntf.o pdb_sprntf.c
mpicc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DMPI -c -o pdb_sscanf.o pdb_sscanf.c
mpicc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DMPI -c -o pdb_write.o pdb_write.c
ar rv libpdb.a pdbrun.o pdb_read.o pdb_sprntf.o pdb_sscanf.o pdb_write.o ms.o
ar: creating libpdb.a
a - pdbrun.o
a - pdb_read.o
a - pdb_sprntf.o
a - pdb_sscanf.o
a - pdb_write.o
a - ms.o
ranlib libpdb.a
mv libpdb.a /programs/gpu/mmpbsa_test/amber12/lib
make[1]: Leaving directory `/programs/gpu/mmpbsa_test/amber12/AmberTools/src/ptraj/pdb'
cd ../arpack && make
make[1]: Entering directory `/programs/gpu/mmpbsa_test/amber12/AmberTools/src/arpack'
make[1]: Nothing to be done for `install'.
make[1]: Leaving directory `/programs/gpu/mmpbsa_test/amber12/AmberTools/src/arpack'
mpicc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DMPI -I/programs/gpu/mmpbsa_test/amber12/include -o main.o main.c
In file included from ptraj.h:80,
                 from main.c:114:
netcdf_ptraj.h:4:39: error: ../../include/pnetcdf.h: No such file or directory
In file included from ptraj.h:80,
                 from main.c:114:
netcdf_ptraj.h:18: error: expected declaration specifiers or ‘...’ before ‘nc_type’
make: *** [main.o] Error 1
[installer.tolkien ptraj]$

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Received on Wed May 02 2012 - 12:30:04 PDT
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