2010/8/28 Andrew Voronkov <drugdesign.yandex.ru>:
> Hm, now it seems like the task is finished, but the output file is not written, here is the output:
Just to be specific, you mean that the file
'/home/voronkov/RMS/fzd5-7_w_prod1.rms' is not written? From the
output you posted it looks like ptraj completed without any errors.
Since you had mentioned that ptraj completes on the head node fine,
this makes me suspect there is some issue with the cluster. Are you
certain that the cluster nodes have access to the '/home/voronkov'
directory? Since I'm not familiar with how your cluster is set up you
may want to check with the cluster's system administrator.
-Dan
>
> \-/
> -/- PTRAJ: a utility for processing trajectory files
> /-\
> \-/ Version: "AMBER 10.0 integrated" (2/15/2008)
> -/- Executable is: "ptraj"
> /-\
> \-/ Residue labels:
>
> ALA PRO VAL CYX GLN GLU ILE THR VAL PRO
> MET CYX ARG GLY ILE GLY TYR ASN LEU THR
> HIE MET PRO ASN GLN PHE ASN HIE ASP THR
> GLN ASP GLU ALA GLY LEU GLU VAL HIE GLN
> PHE TRP PRO LEU VAL GLU ILE GLN CYX SER
> PRO ASP LEU ARG PHE PHE LEU CYX SER MET
> TYR THR PRO ILE CYX LEU PRO ASP TYR HIE
> LYS PRO LEU PRO PRO CYX ARG SER VAL CYX
> GLU ARG ALA LYS ALA GLY CYX SER PRO LEU
> MET ARG GLN TYR GLY PHE ALA TRP PRO GLU
> ARG MET SER CYX ASP ARG LEU PRO VAL LEU
> GLY ARG ASP ALA GLU VAL LEU CYX MET ASP
> TYR ASN ARG ALA PRO VAL CYX GLN GLU ILE
> THR VAL PRO MET CYX ARG GLY ILE GLY TYR
> ASN LEU THR HIE MET PRO ASN GLN PHE ASN
> HIE ASP THR GLN ASP GLU ALA GLY LEU GLU
> VAL HIE GLN PHE TRP PRO LEU VAL GLU ILE
> GLN CYX SER PRO ASP LEU ARG PHE PHE LEU
> CYX SER MET TYR THR PRO ILE CYX LEU PRO
> ASP TYR HIE LYS PRO LEU PRO PRO CYX ARG
> SER VAL CYX GLU ARG ALA LYS ALA GLY CYX
> SER PRO LEU MET ARG GLN TYR GLY PHE ALA
> TRP PRO GLU ARG MET SER CYX ASP ARG LEU
> PRO VAL LEU GLY ARG ASP ALA GLU VAL LEU
> CYX MET ASP TYR ASN ARG Na+ Na+ Na+ Na+
> Na+ Na+ WAT WAT WAT WAT WAT WAT WAT WAT
> WAT WAT WAT WAT WAT WAT WAT WAT WAT WAT
> ...
> WAT
>
> Setting box to be an exact truncated octahedron, angle is 109.471221
>
> PTRAJ: Processing input from file fzd5_w_ca.calc_rms
>
> PTRAJ: trajin fzd5-7_w_prod1.mdcrd
> Checking coordinates: fzd5-7_w_prod1.mdcrd
>
> PTRAJ: trajin fzd5-7_w_prod2.mdcrd
> Checking coordinates: fzd5-7_w_prod2.mdcrd
>
> PTRAJ: trajin fzd5-7_w_prod3.mdcrd
> Checking coordinates: fzd5-7_w_prod3.mdcrd
>
> PTRAJ: trajin fzd5-7_w_prod4.mdcrd
> Checking coordinates: fzd5-7_w_prod4.mdcrd
>
> PTRAJ: rms first mass out /home/voronkov/RMS/fzd5-7_w_prod1.rms .CA time 10
> Mask [.CA] represents 246 atoms
> [No output trajectory specified (trajout)]
>
> PTRAJ: Successfully read the input file.
> Coordinate processing will occur on 1800 frames.
> Summary of I/O and actions follows:
>
> INPUT COORDINATE FILES
> File (fzd5-7_w_prod1.mdcrd) is an AMBER trajectory (with box info) with 481 sets
> File (fzd5-7_w_prod2.mdcrd) is an AMBER trajectory (with box info) with 464 sets
> File (fzd5-7_w_prod3.mdcrd) is an AMBER trajectory (with box info) with 471 sets
> File (fzd5-7_w_prod4.mdcrd) is an AMBER trajectory (with box info) with 384 sets
>
> NO OUTPUT COORDINATE FILE WAS SPECIFIED
>
> ACTIONS
> 1> RMS to first frame using mass weighting
> Dumping RMSd vs. time (with time interval 10.00) to a file named /home/voronkov/RMS/fzd5-7_w_prod1.rms
> Atom selection follows :1-246.CA
>
>
> Processing AMBER trajectory file fzd5-7_w_prod1.mdcrd
>
> Set 1 .................................................
> Set 50 .................................................
> Set 100 .................................................
> Set 150 .................................................
> Set 200 .................................................
> Set 250 .................................................
> Set 300 .................................................
> Set 350 .................................................
> Set 400 .................................................
> Set 450 ...............................
> Processing AMBER trajectory file fzd5-7_w_prod2.mdcrd
>
> Set 1 .................................................
> Set 50 .................................................
> Set 100 .................................................
> Set 150 .................................................
> Set 200 .................................................
> Set 250 .................................................
> Set 300 .................................................
> Set 350 .................................................
> Set 400 .................................................
> Set 450 ..............
> Processing AMBER trajectory file fzd5-7_w_prod3.mdcrd
>
> Set 1 .................................................
> Set 50 .................................................
> Set 100 .................................................
> Set 150 .................................................
> Set 200 .................................................
> Set 250 .................................................
> Set 300 .................................................
> Set 350 .................................................
> Set 400 .................................................
> Set 450 .....................
> Processing AMBER trajectory file fzd5-7_w_prod4.mdcrd
>
> Set 1 .................................................
> Set 50 .................................................
> Set 100 .................................................
> Set 150 .................................................
> Set 200 .................................................
> Set 250 .................................................
> Set 300 .................................................
> Set 350 ..................................
>
> PTRAJ: Successfully read in 1800 sets and processed 1800 sets.
> Dumping accumulated results (if any)
>
> PTRAJ RMS: dumping RMSd vs time data
> Connection to node-56-07 closed.
>
>
> 28.08.10, 16:54, "Daniel Roe" <daniel.r.roe.gmail.com>:
>
>> That certainly is strange behavior. One reason this might be happening
>> is you are directing your input file in as standard input, which in
>> the context of having to submit with another command (mpirun) could be
>> causing strange behavior; the ptraj input file might be redirected to
>> mpirun instead of ptraj. In particular this seems odd:
>>
>> > Connection to node-25-06 closed by remote host.
>> > Connection to node-25-06 closed.
>>
>> Try running ptraj without the redirect operator:
>>
>> mpirun -as single -np 1 -maxtime 360 ptraj fzd5-7_w.prmtop fzd5_w_ca.calc_rms
>>
>> Also, I would recommend you upgrade to AmberTools 1.4
>> (http://ambermd.org/#AmberTools). There are significant performance
>> improvements when compared to amber 10 ptraj. If you do decide to run
>> AT1.4, be sure to apply all bugfixes after downloading
>> (http://ambermd.org/bugfixesat.html).
>>
>> Let me know if you have any more issues - good luck!
>>
>> -Dan
>>
>> On Sat, Aug 28, 2010 at 7:33 AM, Andrew Voronkov wrote:
>> > This is Amber10 package. About compillers I am not sure, but this is single processor run, not parallel, mpirun I just use to submit it in the queue on cluster according to description on how single processor mode should be run there. System has about 250 amino acids, four trajectories, each 5 ns. Only rms Ca calculation for now. When I don't use mpirun - on central node it takes just few minutes to the task to be completed, but there is pretty much trajectories and running software on central node is not tolerated by administration and from other side I want to put all trajectories analysis in the shell script.
>> > Here is calc_rms file:
>> > trajin fzd5-7_w_prod1.mdcrd
>> > trajin fzd5-7_w_prod2.mdcrd
>> > trajin fzd5-7_w_prod3.mdcrd
>> > trajin fzd5-7_w_prod4.mdcrd
>> > rms first mass out /home/voronkov/RMS/fzd5-7_w_prod1.rms .CA time 10
>> >
>> > Here is cluster lof file ptraj.out-114713:
>> >
>> > \-/
>> > -/- PTRAJ: a utility for processing trajectory files
>> > /-\
>> > \-/ Version: "AMBER 10.0 integrated" (2/15/2008)
>> > -/- Executable is: "ptraj"
>> > /-\
>> > \-/ Residue labels:
>> >
>> > ALA PRO VAL CYX GLN GLU ILE THR VAL PRO
>> > MET CYX ARG GLY ILE GLY TYR ASN LEU THR
>> > HIE MET PRO ASN GLN PHE ASN HIE ASP THR
>> > GLN ASP GLU ALA GLY LEU GLU VAL HIE GLN
>> > PHE TRP PRO LEU VAL GLU ILE GLN CYX SER
>> > PRO ASP LEU ARG PHE PHE LEU CYX SER MET
>> > TYR THR PRO ILE CYX LEU PRO ASP TYR HIE
>> > LYS PRO LEU PRO PRO CYX ARG SER VAL CYX
>> > GLU ARG ALA LYS ALA GLY CYX SER PRO LEU
>> > MET ARG GLN TYR GLY PHE ALA TRP PRO GLU
>> > ARG MET SER CYX ASP ARG LEU PRO VAL LEU
>> > GLY ARG ASP ALA GLU VAL LEU CYX MET ASP
>> > TYR ASN ARG ALA PRO VAL CYX GLN GLU ILE
>> > THR VAL PRO MET CYX ARG GLY ILE GLY TYR
>> > ASN LEU THR HIE MET PRO ASN GLN PHE ASN
>> > HIE ASP THR GLN ASP GLU ALA GLY LEU GLU
>> > VAL HIE GLN PHE TRP PRO LEU VAL GLU ILE
>> > GLN CYX SER PRO ASP LEU ARG PHE PHE LEU
>> > CYX SER MET TYR THR PRO ILE CYX LEU PRO
>> > ASP TYR HIE LYS PRO LEU PRO PRO CYX ARG
>> > SER VAL CYX GLU ARG ALA LYS ALA GLY CYX
>> > SER PRO LEU MET ARG GLN TYR GLY PHE ALA
>> > TRP PRO GLU ARG MET SER CYX ASP ARG LEU
>> > PRO VAL LEU GLY ARG ASP ALA GLU VAL LEU
>> > CYX MET ASP TYR ASN ARG Na+ Na+ Na+ Na+
>> > Na+ Na+ WAT WAT WAT WAT WAT WAT WAT WAT
>> > WAT WAT WAT WAT WAT WAT WAT WAT WAT WAT
>> > ...
>> > WAT
>> >
>> > Setting box to be an exact truncated octahedron, angle is 109.471221
>> >
>> > PTRAJ: Processing input from "STDIN" ...
>> > Connection to node-25-06 closed by remote host.
>> > Connection to node-25-06 closed.
>> >
>> >
>> > ptraj.rep-114713
>> >
>> > Task : ptraj
>> > Args : ptraj
>> > Nproc : 1
>> > Exit code: unknown
>> > Note : Time limit exceeded
>> > Output in: /home/voronkov/fzd5-ions-tip3p-1ijy/ptraj.out-114713
>> > Work dir : /home/voronkov/fzd5-ions-tip3p-1ijy
>> > Work time: 6 hours 0 minutes 6 seconds
>> > Started : Fri Aug 27 19:55:33 2010
>> > Nodes : node-25-06:1
>> >
>> >
>> > \-/
>> > -/- PTRAJ: a utility for processing trajectory files
>> > /-\
>> > \-/ Version: "AMBER 10.0 integrated" (2/15/2008)
>> > -/- Executable is: "ptraj"
>> > /-\
>> > \-/ Residue labels:
>> >
>> > ALA PRO VAL CYX GLN GLU ILE THR VAL PRO
>> > MET CYX ARG GLY ILE GLY TYR ASN LEU THR
>> > HIE MET PRO ASN GLN PHE ASN HIE ASP THR
>> > GLN ASP GLU ALA GLY LEU GLU VAL HIE GLN
>> > PHE TRP PRO LEU VAL GLU ILE GLN CYX SER
>> > PRO ASP LEU ARG PHE PHE LEU CYX SER MET
>> > TYR THR PRO ILE CYX LEU PRO ASP TYR HIE
>> > LYS PRO LEU PRO PRO CYX ARG SER VAL CYX
>> > GLU ARG ALA LYS ALA GLY CYX SER PRO LEU
>> > MET ARG GLN TYR GLY PHE ALA TRP PRO GLU
>> > ARG MET SER CYX ASP ARG LEU PRO VAL LEU
>> > GLY ARG ASP ALA GLU VAL LEU CYX MET ASP
>> > TYR ASN ARG ALA PRO VAL CYX GLN GLU ILE
>> > THR VAL PRO MET CYX ARG GLY ILE GLY TYR
>> > ASN LEU THR HIE MET PRO ASN GLN PHE ASN
>> > HIE ASP THR GLN ASP GLU ALA GLY LEU GLU
>> > VAL HIE GLN PHE TRP PRO LEU VAL GLU ILE
>> > GLN CYX SER PRO ASP LEU ARG PHE PHE LEU
>> > CYX SER MET TYR THR PRO ILE CYX LEU PRO
>> > ASP TYR HIE LYS PRO LEU PRO PRO CYX ARG
>> > SER VAL CYX GLU ARG ALA LYS ALA GLY CYX
>> > SER PRO LEU MET ARG GLN TYR GLY PHE ALA
>> > TRP PRO GLU ARG MET SER CYX ASP ARG LEU
>> > PRO VAL LEU GLY ARG ASP ALA GLU VAL LEU
>> > CYX MET ASP TYR ASN ARG Na+ Na+ Na+ Na+
>> > Na+ Na+ WAT WAT WAT WAT WAT WAT WAT WAT
>> > WAT WAT WAT WAT WAT WAT WAT WAT WAT WAT
>> > ...
>> > WAT
>> >
>> > Setting box to be an exact truncated octahedron, angle is 109.471221
>> >
>> > PTRAJ: Processing input from "STDIN" ...
>> > Connection to node-12-10 closed by remote host.
>> > Connection to node-12-10 closed.
>> >
>> >
>> > 28.08.10, 00:08, "Daniel Roe" :
>> >
>> >> It's difficult to comment in too much detail based on the information
>> >> you have given. What version of ptraj are you running, and what
>> >> compilers did you use to build it? How big is the system you are
>> >> running ptraj on, and how long is the trajectory you are processing?
>> >> What sort of actions are you performing (I assume at least an RMSD
>> >> calculation from the name of your input file). What output does ptraj
>> >> give, if any? Also, why are you using 'mpirun' for a single processor
>> >> job? If you don't use 'mpirun' does it complete faster?
>> >>
>> >> -Dan
>> >>
>> >> On Fri, Aug 27, 2010 at 12:33 PM, Andrew Voronkov wrote:
>> >> > It's a bit strange but while running on clusted in a single processor mode ptraj runs for hours:
>> >> > mpirun -as single -np 1 -maxtime 360 ptraj fzd5-7_w.prmtop < fzd5_w_ca.calc_rms
>> >> > while on central node just several minutes.
>> >> > I am not sure if this is a question to Amber mailing list or cluster admins, but I don't understand what causes such a difference.
>> >> >
>> >> > Sincerely yours,
>> >> > Andrew
>> >> >
>> >> > _______________________________________________
>> >> > AMBER mailing list
>> >> > AMBER.ambermd.org
>> >> > http://lists.ambermd.org/mailman/listinfo/amber
>> >> >
>> >>
>> >> _______________________________________________
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>> >>
>> >>
>> >
>> > _______________________________________________
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>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>>
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Received on Sat Aug 28 2010 - 16:00:04 PDT
