Please do not comment on the
> rfree: Error decoding variable 2 2 from:
issue in this thread, I'll create another topic for that in some minutes.
Thanks,
Jan-Philip
On 10/05/2011 12:54 PM, Jan-Philip Gehrcke wrote:
> Hey,
>
> for the first time I have been trying to run MMPBSA.py.MPI (from AT 1.5,
> together with sander 10). For this test case, I used the settings
>
> &general
> startframe = 1000,
> endframe = 1020,
> interval = 5,
> receptor_mask = :107-311,
> ligand_mask = :1-106,312-355
> /
> &gb
> igb = 5,
> /
> &decomp
> idecomp = 1,
> dec_verbose = 3
> /
>
>
> and ran into some problems indicated below (comments inbetween):
>
> 1) first run
> ============
>
> $ mpirun -np 4 MMPBSA.MPI -i mmpbsa_decomp.in -cp
> complex_unsolvated.prmtop -sp ../topology.top -rp receptor.prmtop -lp
> ligand.prmtop -y ../md_equilibrate_00*
>
> Running MMPBSA.MPI on 4 processors...
> Reading command-line arguments and input files...
> Loading and checking parameter files for compatibility...
> Warning: Problem parsing L-J 6-12 parameters.
> Warning: Problem parsing L-J 6-12 parameters.
> Warning: Problem parsing L-J 6-12 parameters.
> ptraj found! Using /home/bioinfp/jang/apps/amber11/bin/ptraj
> sander found! Using /apps11/bioinfp/amber10+/bin/sander for GB calculations
> Warning: Decomposition is only automated if I guess the ligand and receptor
> masks! I will write skeleton mdin files which you must edit. Re-run
> MMPBSA.py with -use-mdins, or allow me to guess the masks.
> Warning: Problem parsing L-J 6-12 parameters.
>
>
>
> * Comment:
> What does the warning regarding the Lennard Jones parameters mean?
>
>
> 2) second run (with -use-mdins)
> ===============================
>
> $ mpirun -np 4 MMPBSA.MPI -i mmpbsa_decomp.in -cp
> complex_unsolvated.prmtop -sp ../topology.top -rp receptor.prmtop -lp
> ligand.prmtop -use-mdins -y ../md_equilibrate_00*
>
> Running MMPBSA.MPI on 4 processors...
> Reading command-line arguments and input files...
> Loading and checking parameter files for compatibility...
> Warning: Problem parsing L-J 6-12 parameters.
> Warning: Problem parsing L-J 6-12 parameters.
> Warning: Problem parsing L-J 6-12 parameters.
> Warning: Problem parsing L-J 6-12 parameters.
> ptraj found! Using /home/bioinfp/jang/apps/amber11/bin/ptraj
> sander found! Using /apps11/bioinfp/amber10+/bin/sander for GB calculations
> Preparing trajectories for simulation...
> 20 frames were read in and processed by ptraj for use in calculation.
>
> Beginning GB calculations with sander...
> calculating complex contribution...
> close failed in file object destructor:
> IOError: [Errno 9] Bad file descriptor
> close failed in file object destructor:
> IOError: [Errno 9] Bad file descriptor
> close failed in file object destructor:
> IOError: [Errno 9] Bad file descriptor
>
>
> * Comment:
> 3 Python IOErrors. But, unfortunately, without the full Python
> Traceback. Why is it not printed here? Maybe due to a too catchy
> try/except block? Close attempts fail three times, because the file
> descriptors are already invalid. Looks one of the four MPI processes
> wins, closes the file(s) and the other three fail...
>
> 3) third run (directly after the second, with the same arguments)
> =================================================================
>
> $ mpirun -np 4 MMPBSA.MPI -i mmpbsa_decomp.in -cp
> complex_unsolvated.prmtop -sp ../topology.top -rp receptor.prmtop -lp
> ligand.prmtop -use-mdins -y ../md_equilibrate_00*
>
> Running MMPBSA.MPI on 4 processors...
> Reading command-line arguments and input files...
> Loading and checking parameter files for compatibility...
> Warning: Problem parsing L-J 6-12 parameters.
> ptraj found! Using /home/bioinfp/jang/apps/amber11/bin/ptraj
> sander found! Using /apps11/bioinfp/amber10+/bin/sander for GB calculations
> Warning: Problem parsing L-J 6-12 parameters.
> Warning: Problem parsing L-J 6-12 parameters.
> Warning: Problem parsing L-J 6-12 parameters.
> Preparing trajectories for simulation...
> 20 frames were read in and processed by ptraj for use in calculation.
>
> Beginning GB calculations with sander...
> calculating complex contribution...
> close failed in file object destructor:
> IOError: [Errno 9] Bad file descriptor
>
> * Comment:
> only one IOError left. Hmm.. this time-dependency is strange and could
> be related to our NFS setup? The situation may have improved due to
> files that have already been created during the second run. I don't know.
>
> 4) fourth run (directly after the third)
> ========================================
> $ mpirun -np 4 MMPBSA.MPI -i mmpbsa_decomp.in -cp
> complex_unsolvated.prmtop -sp ../topology.top -rp receptor.prmtop -lp
> ligand.prmtop -use-mdins -y ../md_equilibrate_00*
>
> Running MMPBSA.MPI on 4 processors...
> Reading command-line arguments and input files...
> Loading and checking parameter files for compatibility...
> Warning: Problem parsing L-J 6-12 parameters.
> ptraj found! Using /home/bioinfp/jang/apps/amber11/bin/ptraj
> Warning: Problem parsing L-J 6-12 parameters.
> sander found! Using /apps11/bioinfp/amber10+/bin/sander for GB calculations
> Warning: Problem parsing L-J 6-12 parameters.
> Warning: Problem parsing L-J 6-12 parameters.
> Preparing trajectories for simulation...
> 20 frames were read in and processed by ptraj for use in calculation.
>
> Beginning GB calculations with sander...
> calculating complex contribution...
>
> * Comment:
> Now, things looked fine and I left the office
>
>
> 5) next morning
> ===============
>
> Still at
>
> calculating complex contribution...
>
> with python having 100 % CPU usage and no other heavy-cpu-using processes.
>
> _MMPBSA_complex_gb.mdout.0 (attached) was last changed at approximately
> the same time as MMPBSA run 4 started. So I killed the mpirun. The last
> lines of _MMPBSA_complex_gb.mdout.0:
>
>
>> rfree: Error decoding variable 2 2 from:
>> RES EDIT
>>
>> this indicates that your input contains
>>
>> incorrect information
>>
>> field 2 was supposed to
>>
>> have a (1=character, 2=integer, 3=decimal) value
>
> In `utils.sandercalc`, I printed the sander command:
>
> /apps11/bioinfp/amber10+/bin/sander -O -i _MMPBSA_gb_decomp_com.mdin -o
> _MMPBSA_complex_gb.mdout.0 -p complex_unsolvated.prmtop -c
> _MMPBSA_dummycomplex.inpcrd.1 -y _MMPBSA_complex.mdcrd.0 -r
> _MMPBSA_.restrt.0
>
> I ran it independently and it almost immediately returned, creating the
> same .mdout file as attached. Hence, in case (4) from above,
> MMPBSA.py.MPI had a problem detecting this and ended up in some endless
> loop responsible for 100 % CPU usage.
>
> Btw: In `utils.sandercalc`, `os.system` is used to run the sander
> process -- which is considered to be a deprecated way. One could think
> about using Python's subprocess module in the future (one advantage is
> being able to receive the stdout/stderr of the subprocess).
>
>
> Summary
> =======
> - Something irritated MMPBSA.py.MPI so it opened/accessed/closed files
> in the wrong order. Difficult to debug due to missing Python tracebacks
> and potential dependency on NFS.
> - Some input makes sander fail, which was not properly handled by
> MMPBSA.py.MPI (endless loop). Also difficult to debug, but you may know
> what's wrong with my input.
> - There is another problem with my input leading to the warning about
> parsing L-J 6-12 parameters.
>
> Btw:
> Why is the ./AmberTools/src/mmpbsa_py/MMPBSA_mods/utils.py the one that
> is relevant during runtime, while changes in
> /lib/python2.6/site-packages/MMPBSA_mods/utils.py do not have an effect?
> Shouldn't it be the other way round?
>
>
> Hope that someone can help me out here!
>
> Thanks,
>
> Jan-Philip
>
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Received on Wed Oct 05 2011 - 07:00:03 PDT
