Re: [AMBER] Performed MMPBSA.py.MPI failed in Amber16 with Ambertools 17

From: Jiyuan Liu <liujiyuan.nwsuaf.edu.cn>
Date: Mon, 21 Aug 2017 22:22:48 +0800

2017/8/21 19:40, David A Case д:
> On Sun, Aug 20, 2017, Jiyuan Liu wrote:
>> I have reinstalled AMBER16, and accepted to install minniconda as the same
>> as the first time installation. The MMPBSA.py.MPI could be performed in
>> parallel at this time. I thought the only difference between these two times
>> installation was the configure of mpich2 v3.1.4,
>>
>> in the first time the configure parameter was "./confifgure
>> --prefix=/usr/local/mpich2 CFLAGS=-fPIC --enable-shared FC=ifort CC=icc",
>> and the second time parameter was "./configure CC=icc CXX=icpc FC=ifort
>> F77=ifort CFLAGS="-fPIC" CXXFLAGS="-fPIC" FFLAGS="-fPIC" --enable-shared
>> --prefix=/usr/local/mpich2". Would ask you whether the configure parameter
>> of mpich2 could cause the parallel of MMPBSA.py.MPI abnormal?
> Good news, and thanks for the report. I was wrong in my earlier email:
> Amber's configure script builds mpi4py, and how that gets done depends upon
> the mpi installation. I'm not familiar enough with this to know why your
> first time failed.
>
> Our main hope (and expectation) is if that users install mpi via the
> configure_mpich command, that that path will work with mpi4py.


I will try to install mpi via configure_mpich script when the AMBER16
has the new bugfix.


>> I found a new problem with MMPBSA.py.MPI, when I prepare to perform it, I
>> must type a command "source $AMBERHOME/amber16.sh before. However I have
>> added the environment parameter in the .bashrc.
> Double check everything: is your .bashrc being executed on login? It's not
> clear what you really mean when you say that you "added the environment
> parameter": what environment parameter? You actually have to have the
> "source" command in the startup scripts.

I have added "export AMBERHOME=/amber16",and "source /amber16/amber.sh"
in ~/.bashrc, but when I want to perform MMPBSA.py.MPI, I needed to
source $AMBERHOME/amber.sh before.

>
> Others may comment on the clustering problems in cpptraj. You might need
> to re-post that problem with a subject indicating you are having trouble
> with cpptraj. Otherwise, the people that know the answer might not even
> read your email.


I will post the problem in the new subject. Thank you so much for your
reminding.


Jiyuan








> .....dac
>
>
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Received on Mon Aug 21 2017 - 07:30:02 PDT
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