Hi,
On Wed, Apr 1, 2015 at 7:35 AM, Abhishek TYAGI <atyagiaa.connect.ust.hk> wrote:
> cpptraj found! Using /ghome/atyagiaa/amber14/bin/cpptraj
>
> Preparing trajectories for simulation...
>
> /d4/atyagiaa/amber14/bin/MMPBSA_mods/make_trajs.py:631: UserWarning: Solvated topology 0 has IFBOX == 0
>
> warn('Solvated topology %s has IFBOX == 0' % ifbox)
>
> Error: Only 'ensemble' mode supported in parallel.
It seems like somehow your cpptraj was built with MPI but ended up not
being named cpptraj.MPI. What were the exact steps you used to
configure and build amber?
-Dan
>
> File "/ghome/atyagiaa/amber14/bin/MMPBSA.py.MPI", line 95, in <module>
>
> app.file_setup()
>
> File "/d4/atyagiaa/amber14/bin/MMPBSA_mods/main.py", line 156, in file_setup
>
> self.mpi_size, str(external_progs['cpptraj']), self.pre)
>
> File "/d4/atyagiaa/amber14/bin/MMPBSA_mods/make_trajs.py", line 134, in make_trajectories
>
> traj.Run(pre + 'normal_traj_cpptraj.out')
>
> File "/d4/atyagiaa/amber14/bin/MMPBSA_mods/make_trajs.py", line 684, in Run
>
> raise TrajError('Error running %s' % self.program)
>
> AttributeError: 'Trajectory' object has no attribute 'program'
>
> Exiting. All files have been retained.
>
> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
>
>
> The error is repeatedly coming, the DO_PARRALLEL used for -np 8, before running the script.
>
> Could you please suggest me what could be the desired solution for this problem.
>
>
> One more thing I performed MD using NAMD, than converted my files using chamber. One more thing these files easily running on serial version of ambertool14.
>
>
> Thanks in advance
>
>
> Abhi
>
>
> ________________________________
> From: Abhishek Tyagi <atyagiaa.connect.ust.hk>
> Sent: Saturday, March 28, 2015 12:39 AM
> To: amber.ambermd.org
> Subject: Re: MMPBSA error
>
> Hi,
>
> this is running on gnu cluster on serial installation, I found that for the first problem when i set igb=1, MMGBSA is running, but when it is set igb=5, it shows the error
>
> File "/ghome/atyagiaa/amber14/bin/MMPBSA.py", line 96, in <module>
> app.run_mmpbsa()
> File "/d4/atyagiaa/amber14/bin/MMPBSA_mods/main.py", line 218, in run_mmpbsa
> self.calc_list.run(rank, self.stdout)
> File "/d4/atyagiaa/amber14/bin/MMPBSA_mods/calculation.py", line 79, in run
> calc.run(rank, stdout=stdout, stderr=stderr)
> File "/d4/atyagiaa/amber14/bin/MMPBSA_mods/calculation.py", line 148, in run
> self.prmtop))
> CalcError: /ghome/atyagiaa/amber14/bin/sander failed with prmtop complex.prmtop!
> Exiting. All files have been retained.
>
> for the second problem: I have followed the installation guide as follows:
>
> ./configure -mpi gnu
> make install
> export DO_PARALLEL='mpirun -np 16’
> make test.parallel
>
> everything finished fine, but when I had checked AMBERHOME/bin/ their is no MMPBSA.py.MPI file in the folder.
>
> what could be the reason
>
> Thanks in advance
>
> Abhi
>
>
>
> ~
> On 27 Mar, 2015, at 3:00 am, amber-request.ambermd.org<mailto:amber-request.ambermd.org> wrote:
>
> ------------------------------
>
> Message: 15
> Date: Thu, 26 Mar 2015 08:55:35 -0400
> From: Kenneth Huang <kennethneltharion.gmail.com<mailto:kennethneltharion.gmail.com>>
> Subject: [AMBER] MMGBSA error
> To: AMBER Mailing List <amber.ambermd.org<mailto:amber.ambermd.org>>
> Message-ID:
> <CALeh7kBoAEw+CLHBu6USEDxeRu6wYW98Wjy_tyvOnpNpfrLhXA.mail.gmail.com<mailto:CALeh7kBoAEw+CLHBu6USEDxeRu6wYW98Wjy_tyvOnpNpfrLhXA.mail.gmail.com>>
> Content-Type: text/plain; charset=UTF-8
>
> Abhi,
>
> What's the exact error it's giving on the GPU cluster? And have you checked
> the _MMPBSA_complex_gb.mdout file to see if there's a description of
> what's specifically going wrong?
>
>
> For your second problem, I'm guessing it's because you haven't compiled
> Amber in mpi- you can use the below in the Amber directory.
>
> ./configure -mpi gnu
> make install
>
> Best,
>
> Kenneth
>
> On Thu, Mar 26, 2015 at 2:06 AM, Abhishek TYAGI <atyagiaa.connect.ust.hk<mailto:atyagiaa.connect.ust.hk>
> <javascript:_e(%7B%7D,'cvml','atyagiaa.connect.ust.hk<mailto:atyagiaa.connect.ust.hk>');>> wrote:
>
> Hi,
>
>
> I have following questions:
>
>
> 1. I am using MMGBSA for receptor-ligand interaction, the calculations
> successfully finished on my PC, but when i tried on GPU cluster, I was not
> able to run it, for the similar files, it shows error for complex.
>
>
> 2. Second problem is with mpi, i had installed on the gpu cluster
> following the installation guidance provided in the Amber manual, and I
> have not found MMPBSA.py.MPI on my bin directory.
>
>
> Could anyone suggest me what could be the error
>
>
> Thanks? in advance
>
>
> Abhi
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>
>
>
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
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Received on Wed Apr 01 2015 - 07:30:04 PDT
