{Spam?} Re: [gmx-users] Re: wierd behavior of mdrun
Justin A. Lemkul
jalemkul at vt.edu
Tue Sep 8 22:18:42 CEST 2009
This is not a Gromacs issue. You should take it up with your sysadmin. Perhaps
you are seeing sporadic successes and failures due to a buggy node (or
multiple!) or perhaps you have typos in your submission script.
-Justin
Paymon Pirzadeh wrote:
> OK! I tested your suggestion about frequent output. As you had
> predicted, it crashed immediately. But the message I got from the
> cluster was
>
> PBS Job Id: 94865.orca1.ibb
> Job Name: AFPIII_NVT275test
> job deleted
> Job deleted at request of root at elder2.ibb
> MOAB_INFO: job was rejected - job violates qos configuration 'job
> '94865' violates MINPROC policy of 4 (R: 1, U: 0)'
>
> This is despite the fact that in my submission script, the number of
> CPUs are 8! As I had mentioned earlier, same script is used for my water
> systems.
> Regards,
>
> Payman
>
>
>
>
> On Fri, 2009-09-04 at 19:29 -0400, Justin A. Lemkul wrote:
>> Have you tried my suggestion from the last message of setting frequent output?
>> Could your system just be collapsing at the outset of the simulation? Setting
>> nstxout = 1 would catch something like this.
>>
>> There is nothing special about treating a protein in parallel vs. a system of
>> water. Since a system of water runs just fine, it seems even more likely to me
>> that your system is simply crashing immediately, rather than a problem with
>> Gromacs or the MPI implementation.
>>
>> -Justin
>>
>> Paymon Pirzadeh wrote:
>>> Regarding the problems I have on running protein system in parallel
>>> (runs without output), When I run pure water system, everything is fine,
>>> I have tested pure water systems 8 times larger than my protein system.
>>> while the former runs fine, the latter has problems. I have also tested
>>> pure water systems with approximately same number of sites in .gro file
>>> as in my protein .gro file, and with the same input file in terms of
>>> spitting outputs; they are fine.I would like to know what happens to
>>> GROMACS when a protein is added to the system. The cluster admin has not
>>> get back to me, but I still want to check there is no problem with my
>>> setup! (although my system runs fine in serial mode).
>>> Regards,
>>>
>>> Payman
>>>
>>>
>>>
>>> On Fri, 2009-08-28 at 16:41 -0400, Justin A. Lemkul wrote:
>>>> Payman Pirzadeh wrote:
>>>>> There is sth strange about this problem which I suspect it might be due to
>>>>> the mdp file and input. I can run the energy minimization without any
>>>>> problems (I submit the job and it apparently works using the same submission
>>>>> script)! But as soon as I prepare the tpr file for MD run, then I run into
>>>>> this run-without-output trouble.
>>>>> Again I paste my mdp file below (I want to run an NVT run):
>>>>>
>>>> There isn't anything in the .mdp file that suggests you wouldn't get any output.
>>>> The output of mdrun is buffered, so depending on your settings, you may have
>>>> more frequent output during energy minimization. There may be some problem with
>>>> the MPI implementation in buffering and communicating data properly. That's a
>>>> bit of a guess, but it could be happening.
>>>>
>>>> Definitely check with the cluster admin to see if there are any error messages
>>>> reported for the jobs you submitted.
>>>>
>>>> Another test you could do to force a huge amount of data would be to set all of
>>>> your outputs (nstxout, nstxtcout, etc) = 1 and run a much shorter simulation (to
>>>> prevent massive data output!); this would force more continuous data through the
>>>> buffer.
>>>>
>>>> -Justin
>>>>
>>>>> cpp = cpp
>>>>> include = -I../top
>>>>> define = -DPOSRES
>>>>>
>>>>> ; Run control
>>>>>
>>>>> integrator = md
>>>>> dt = 0.001 ;1 fs
>>>>> nsteps = 3000000 ;3 ns
>>>>> comm_mode = linear
>>>>> nstcomm = 1
>>>>>
>>>>> ;Output control
>>>>>
>>>>> nstxout = 5000
>>>>> nstlog = 5000
>>>>> nstenergy = 5000
>>>>> nstxtcout = 1500
>>>>> nstvout = 5000
>>>>> nstfout = 5000
>>>>> xtc_grps =
>>>>> energygrps =
>>>>>
>>>>> ; Neighbour Searching
>>>>>
>>>>> nstlist = 10
>>>>> ns_type = grid
>>>>> rlist = 0.9
>>>>> pbc = xyz
>>>>>
>>>>> ; Electrostatistics
>>>>>
>>>>> coulombtype = PME
>>>>> rcoulomb = 0.9
>>>>> ;epsilon_r = 1
>>>>>
>>>>> ; Vdw
>>>>>
>>>>> vdwtype = cut-off
>>>>> rvdw = 1.2
>>>>> DispCorr = EnerPres
>>>>>
>>>>> ;Ewald
>>>>>
>>>>> fourierspacing = 0.12
>>>>> pme_order = 4
>>>>> ewald_rtol = 1e-6
>>>>> optimize_fft = yes
>>>>>
>>>>> ; Temperature coupling
>>>>>
>>>>> tcoupl = v-rescale
>>>>> ld_seed = -1
>>>>> tc-grps = System
>>>>> tau_t = 0.1
>>>>> ref_t = 275
>>>>>
>>>>> ; Pressure Coupling
>>>>>
>>>>> Pcoupl = no
>>>>> ;Pcoupltype = isotropic
>>>>> ;tau_p = 1.0
>>>>> ;compressibility = 5.5e-5
>>>>> ;ref_p = 1.0
>>>>> gen_vel = yes
>>>>> gen_temp = 275
>>>>> gen_seed = 173529
>>>>> constraint-algorithm = Lincs
>>>>> constraints = all-bonds
>>>>> lincs-order = 4
>>>>>
>>>>> Regards,
>>>>>
>>>>> Payman
>>>>>
>>>>>
>>>>> -----Original Message-----
>>>>> From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
>>>>> On Behalf Of Mark Abraham
>>>>> Sent: August 27, 2009 3:32 PM
>>>>> To: Discussion list for GROMACS users
>>>>> Subject: Re: [gmx-users] Re: wierd behavior of mdrun
>>>>>
>>>>> Vitaly V. Chaban wrote:
>>>>>> Then I believe you have problems with MPI.
>>>>>>
>>>>>> Before I experienced something alike on our old system - serial
>>>>>> version worked OK but parallel one failed. The same issue was with
>>>>>> CPMD by the way. Another programs worked fine. I didn't correct that
>>>>>> problem...
>>>>>>
>>>>>> On Thu, Aug 27, 2009 at 7:14 PM, Paymon Pirzadeh<ppirzade at ucalgary.ca>
>>>>> wrote:
>>>>>>> Yes,
>>>>>>> it works when it is run on one processor interactively!
>>>>> That's fine, but it doesn't mean the problem is with the parallelism, as
>>>>> Vitaly suggests. If your cluster filesystem isn't configured properly,
>>>>> you will observe these symptoms. Since the submission script was the
>>>>> same, MPI worked previously, so isn't likely to be the problem...
>>>>>
>>>>> Mark
>>>>>
>>>>>>> On Thu, 2009-08-27 at 09:23 +0300, Vitaly V. Chaban wrote:
>>>>>>>>> I made a .tpr file for my md run without any problems (using the bottom
>>>>>>>>> mdp file). My job submission script is also the same thing I used for
>>>>>>>>> other jobs which had no problems. But now when I submit this .tpr file,
>>>>>>>>> only an empty log file is generated! The qstat of the cluster shows
>>>>> that
>>>>>>>>> the job is running, also the processors are 100% engaged while I have
>>>>> no
>>>>>>>>> outputs!
>>>>>>>> A standard guess: what about trying to run the single-processor job on
>>>>>>>> the same cluster? Does it run OK?
>>>>>>>>
>>>>>>>>
>>>>>> _______________________________________________
>>>>>> gmx-users mailing list gmx-users at gromacs.org
>>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>>>> Please search the archive at http://www.gromacs.org/search before posting!
>>>>>> Please don't post (un)subscribe requests to the list. Use the
>>>>>> www interface or send it to gmx-users-request at gromacs.org.
>>>>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>>>>>
>>>>> _______________________________________________
>>>>> gmx-users mailing list gmx-users at gromacs.org
>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>>> Please search the archive at http://www.gromacs.org/search before posting!
>>>>> Please don't post (un)subscribe requests to the list. Use the
>>>>> www interface or send it to gmx-users-request at gromacs.org.
>>>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> gmx-users mailing list gmx-users at gromacs.org
>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>>> Please search the archive at http://www.gromacs.org/search before posting!
>>>>> Please don't post (un)subscribe requests to the list. Use the
>>>>> www interface or send it to gmx-users-request at gromacs.org.
>>>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>>>>
>>>
>
>
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
More information about the gromacs.org_gmx-users
mailing list