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" <daniel.r.roe.gmail.com>:
> 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
> >
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
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Received on Sat Aug 28 2010 - 05:00:03 PDT
