Hi,
in the amber directory I moved to amberhome, all the fles were as follows:
$AMBERHOME/bin/ls
addles hydra_nameserver mpichversion mpirun sander
ante-MMPBSA.py hydra_persist mpicxx mpivars sander.LES.MPI
chemistry hydra_pmi_proxy mpiexec nc-config sander.MPI
compat24.py mdgx.MPI mpiexec.hydra nccopy ucpp
compat24.pyc MMPBSA_mods mpif77 ncdump yacc
cpptraj MMPBSA.py mpif90 ncgen
cpptraj.MPI MMPBSA.py.MPI mpifort ncgen3
fftw-wisdom mpic++ mpinab nf-config
fftw-wisdom-to-conf mpicc mpinab2c parkill
I have followed the instruction avalable in amber14 manual.
Thanks
Abhi
From: Daniel Roe <daniel.r.roe.gmail.com<mailto:daniel.r.roe.gmail.com?Subject=Re%3A%20%5BAMBER%5D%20MMPBSA%20error>>
Date: Wed, 1 Apr 2015 08:13:29 -0600
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
Dear Experts,
I am trying to install MPI version of amber14 and ambertool14 to use MMPBSA on gpu cluster here in my university, the details are as follows:
1. The MMPBSA.py.MPI is in $AMBERHOME/bin/MMPBSA.py.MPI
2. While executing the command
$AMBERHOME/bin/MMPBSA.py.MPI -O -i mmpbsa.in -o out.dat -sp solvated.prmtop -cp complex.prmtop -rp receptor.prmtop -lp ligand.prmtop -y last2.5ns.dcd
Loading and checking parameter files for compatibility...
CHAMBER prmtops found. Forcing use of sander
sander found! Using /ghome/atyagiaa/amber14/bin/sander
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.
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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Received on Mon Apr 06 2015 - 20:30:03 PDT
