Re: [AMBER] segmentation fault when running sander

From: Jason Swails <jason.swails.gmail.com>
Date: Wed, 18 May 2011 14:14:31 -0400

Can you attach your input files? This includes the topology file, inpcrd, and mdin. Segfaults are indicative of memory errors, but it's not at all specific.

There may be something subtly wrong with your topology file, or it may be a bug.

All the best,
Jason

--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
On May 18, 2011, at 1:00 AM, Chinh Su Tran To <chinh.sutranto.gmail.com> wrote:
> Dear Amber users,
> 
> Again i got the same error of "segmentation fault" even whatever i modified
> my batch-file. The "ndm_md1.rst" was not even created.
> 
> I compared the "ndm_md1.out" with other successful runs (i.e other
> "xx_md1.out"), i found that the process of running wat-md1.in was halted in
> the first step, as shown below (this is extracted from the "ndm_md1.out"):
> 
> *NSTEP =        0   TIME(PS) =       0.000  TEMP(K) =     0.00  PRESS =
> 0.0
> Etot   =    -64769.2683  EKtot   =         0.0000  EPtot      =
> -64769.2683
> BOND   =        79.7941  ANGLE   =       500.8945  DIHED      =
> 1498.9190
> 1-4 NB =       453.3799  1-4 EEL =      7256.7348  VDWAALS    =
> 10279.1689
> EELEC  =    -84838.1594  EHBOND  =         0.0000  RESTRAINT  =
> 0.0000
> Ewald error estimate:   0.8471E-04
> ------------------------------------------------------------------------------
> *
> 
> Please help. I really have no idea what is going on. I think the
> "ndm_md1.rst" had not been created because the process stopped unexpectedly.
> 
> Thank you.
> Chinsu
> 
> 
> 
> 
> On Mon, May 16, 2011 at 7:46 PM, Chinh Su Tran To
> <chinh.sutranto.gmail.com>wrote:
> 
>> Dear Jason,
>> 
>> This is my batch file:
>> 
>> */usr/local/amber10/exe/sander -O -i ./file-in/wat-min1.in -o
>> ./results/ndm_min1.out -p ./results/ndm-wat.prmtop -c
>> ./results/ndm-wat.inpcrd -r ./results/ndm_min1.rst -ref
>> ./results/ndm-wat.inpcrd
>> 
>> /usr/local/amber10/exe/sander -O -i ./file-in/wat-min2.in -o
>> ./results/ndm_min2.out -p ./results/ndm-wat.prmtop -c ./results/ndm_min1.rst
>> -r ./results/ndm_min2.rst
>> 
>> 
>> /usr/local/amber10/exe/sander -O -i ./file-in/wat-md1.in -o
>> ./results/ndm_md1.out -p ./results/ndm-wat.prmtop -c ./results/ndm_min2.rst
>> -r ./results/ndm_md1.rst -x ./results/ndm_md1.mdcrd -ref
>> ./results/ndm_min2.rst
>> 
>> /usr/local/amber10/exe/sander -O -i ./file-in/wat-md2.in -o
>> ./results/ndm_md2.out -p ./results/ndm-wat.prmtop -c ./results/ndm_md1.rst
>> -r ./results/ndm_md2.rst -x ./results/ndm_md2.mdcrd
>> 
>> /usr/local/amber10/exe/ambpdb -p ./results/ndm-wat.prmtop <
>> ./results/ndm_md2.rst > ./results/ndm_md2.pdb*
>> 
>> And the part below is the error I got:
>> 
>> 
>> **/var/spool/torque/mom_priv/*
>> *jobs/5731.bircibm.SC <http://5731.bircibm.sc/>: line 17: 14885
>>> Segmentation fault      /usr/local/amber10/exe/sander -O -i ./file-in/
>>> wat-md1.in -o ./results/ndm_md1.out -p ./results/ndm-wat.prmtop -c
>>> ./results/ndm_min2.rst -r ./results/ndm_md1.rst -x
>> ./results/ndm_md1.mdcrd
>>> -ref ./results/ndm_min2.rst
>>> 
>>> Unit   30 Error on OPEN:
>>> ./results/ndm_md1.rst
>>> /var/spool/torque/mom_priv/**jobs/5731.bircibm.SC<http://5731.bircibm.sc/>:
>> line 25:
>>> ./results/ndm_md2.rst: No such file or directory
>> 
>> *
>> I double-checked and found that the ndm_md1.rst was not created, causing
>> the next command was not performed, so the second error led to "could not
>> open the ndm_md2.rst"
>> 
>> I viewed other threads from Amber archive titled "segmentation fault"
>> saying about "molecular size", but i dont think this error was addressed
>> because i ran the similar batch file for other larger molecules and they ran
>> fine.
>> 
>> Is it possible that it was related to the TIP3PBOX of solvent I used? I
>> used TIP3PBOX 12 for this molecule.
>> 
>> Thanks for your reply, and hope more help.
>> 
>> Chinsu
>> 
>> 
>> On Mon, May 16, 2011 at 7:27 PM, Jason Swails <jason.swails.gmail.com>wrote:
>> 
>>> On Mon, May 16, 2011 at 6:42 AM, Chinh Su Tran To
>>> <chinh.sutranto.gmail.com>wrote:
>>> 
>>>> Dear Amber users,
>>>> 
>>>> Below is the error I encountered when running a batch file of sander for
>>> MD
>>>> runs following 2-step minimization:
>>>> 
>>>> */var/spool/torque/mom_priv/jobs/5731.bircibm.SC: line 17: 14885
>>>> Segmentation fault      /usr/local/amber10/exe/sander -O -i ./file-in/
>>>> wat-md1.in -o ./results/ndm_md1.out -p ./results/ndm-wat.prmtop -c
>>>> ./results/ndm_min2.rst -r ./results/ndm_md1.rst -x
>>> ./results/ndm_md1.mdcrd
>>>> -ref ./results/ndm_min2.rst
>>>> 
>>>> Unit   30 Error on OPEN:
>>>> ./results/ndm_md1.rst
>>>> /var/spool/torque/mom_priv/jobs/5731.bircibm.SC: line 25:
>>>> ./results/ndm_md2.rst: No such file or directory
>>>> *
>>>> 
>>> 
>>> I don't think you copied everything over correctly.  Here it says that
>>> ./results/ndm_md2.rst doesn't exist, but I don't see anywhere above where
>>> you used that file.
>>> 
>>> 
>>>> could anyone please give me a hint about this? I just dont understand
>>> why
>>>> it
>>>> happened 'cause it ran fine for other molecules before. And why didnt it
>>>> occur during minimization?
>>>> 
>>>> Thank you very much, and really looking forward to your reply.
>>>> 
>>>> Regards,
>>>> Chinsu
>>>> 
>>>> _______________________________________________
>>>> AMBER mailing list
>>>> AMBER.ambermd.org
>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>> 
>>>> 
>>> 
>>> 
>>> --
>>> Jason M. Swails
>>> Quantum Theory Project,
>>> University of Florida
>>> Ph.D. Candidate
>>> 352-392-4032
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>> 
>> 
>> 
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Received on Wed May 18 2011 - 11:30:03 PDT
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