Dan Roe answered part of your question 6 days ago. His answer is archived here: http://archive.ambermd.org/201412/0021.html <http://archive.ambermd.org/201412/0021.html>.
To reiterate what he said, your problem is here:
[root.HPC ~]# mpif90 -show
ifort -I/opt/mpich2.12/include -I/opt/mpich2.12/include -L/opt/mpich2.12/lib -L/opt/mpich2.12/lib -lmpichf90 -lmpichf90 -lmpich -lopa -lpthread -lrt
[root.HPC ~]# mpicc -show
gcc -I/opt/mpich2.12/include -L/opt/mpich2.12/lib -L/opt/mpich2.12/lib -lmpich -lopa -lpthread –lrt
Your MPI is configured to use the Intel Fortran compiler and the GNU C compiler. This will NOT work for Amber. You need to use an MPI that is configured using *just* the GNU compilers or *just* the Intel compilers. If you are having trouble building an Amber-compatible MPI, you can use the “configure_mpich” or “configure_openmpi” scripts inside $AMBERHOME/AmberTools/src to build an MPI directly inside $AMBERHOME instead.
Your other problems involve some of the tests. In particular, the MMPBSA.py tests seem to fail, but there is not enough information to figure out why. I will try to reproduce this using GCC 4.9 on my own machine and fix it if I can figure out what went wrong. The other failures involve the thermodynamic integration tests for pmemd. So it seems that you cannot use either MMPBSA.py or thermodynamic integration with pmemd using this install.
HTH,
Jason
> On Dec 6, 2014, at 8:42 PM, Dailin Li <lidl.xmut.edu.cn> wrote:
>
>
> Dear Mr/Mrs,
> We have bought Amber14 recently and met problems with installation in parallel on CentOS 5.4 with gcc-4.9.1. Attachements please find seperately the detailed problems, 2014-12-01_11-07-58.diff, 2014-12-01_11-07-58.log, 2014-12-01_09-39-20.log, and at_summary.
>
> I am looking forward to your kind reply. Thank you very much for your help and support.
> Regards,
> Dailin <Problems with amber14 intallation in parallel.doc><2014-12-01_11-07-58.diff><2014-12-01_11-07-58.log><2014-12-01_09-39-20.log><at_summary.txt>_______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Sun Dec 07 2014 - 19:30:02 PST
