Can you try to run "mpirun -n 2" in your head node?
mpirun -np 2 $amber -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.out -sp
PRMT7_WT_NH2.prmtop -cp complex.prmtop -rp receptor.prmtop -lp
peptide.prmtop -y *.crd
If you could, can you see the output?
If yes, it likely relates to your cluster and you need to talk to your
admin.
Hai
On Mon, Jul 11, 2016 at 4:53 PM, Thakur, Abhishek <axt651.miami.edu> wrote:
> Yes I did that and it seems to run fine.
>
> But problem is that if I run serially it put everything on head node and I
> have a time limit for 30 minutes for head node.
>
> So I need to submit it to some queue
>
> For that I am trying to make this script
>
> ________________________________
> From: Hai Nguyen <nhai.qn.gmail.com>
> Sent: Monday, July 11, 2016 9:49:37 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] MMPBSA
>
> how's about .out file?
>
> Have you tried to run serially in your terminal (without submitting to
> cluster)?
>
> Hai
>
> On Mon, Jul 11, 2016 at 4:46 PM, Thakur, Abhishek <axt651.miami.edu>
> wrote:
>
> > There is nothing in it.
> >
> > It is just empty.
> >
> >
> > In my script I generate two files .err and .out
> >
> > #BSUB -n 16
> > #BSUB -q parallel
> > #BSUB -W 168:00
> > #BSUB -J mmpbsa_WT_NH2
> > #BSUB -P prmt
> > #BSUB -o %J.out
> > #BSUB -e %J.err
> >
> > So while running it stops after 2 minutes and i get blank .err file
> >
> >
> > ________________________________
> > From: Hai Nguyen <nhai.qn.gmail.com>
> > Sent: Monday, July 11, 2016 9:41:40 AM
> > To: AMBER Mailing List
> > Subject: Re: [AMBER] MMPBSA
> >
> > it seems that you got lots of trouble with MMPBSA.
> >
> > I suggest you to
> >
> > - read AMBER tutorial, follow it and reproduce it.
> >
> >
> https://urldefense.proofpoint.com/v2/url?u=http-3A__ambermd.org_tutorials_advanced_tutorial3_py-5Fscript_&d=CwICAg&c=y2w-uYmhgFWijp_IQN0DhA&r=0Hah93XWYYBgmROOVcaccg&m=RyzYf2t1iheX3X5v5cYjh5hSoIL2cIiT6gWkJCDIAjA&s=KYP0sLhFNqZRrs4jdRz1IYFH4tNw4ApHBoIOJUNiz_k&e=
> > - Did your amber version pass the tests?
> > - Per your previous emails about MMPBSA: were you issue solved? If not,
> > have you tried to follow corresponding instruction?
> > - more specific: what does 'crash' mean? What is exact error message?
> >
> > Hai
> >
> > On Mon, Jul 11, 2016 at 4:31 PM, Thakur, Abhishek <axt651.miami.edu>
> > wrote:
> >
> > > Hi
> > >
> > > I am trying to do mmpbsa calculation using following script
> > >
> > >
> > > set amber = $AMBERHOME/bin/MMPBSA.py.MPI
> > >
> > > #Write input below
> > > cat > mmpbsa.in << EOF
> > > Input file for running PB
> > > &general
> > > startframe=1, endframe=58750, interval=2,
> > > /
> > > &gb
> > > igb=5, saltcon=0.100,
> > > /
> > > &pb
> > > istrng=0.100,
> > > /
> > >
> > > #Execute MMPBSA job serial version
> > >
> > > mpirun -np 16 $amber -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.out -sp
> > > PRMT7_WT_NH2.prmtop -cp complex.prmtop -rp receptor.prmtop -lp
> > > peptide.prmtop -y *.crd
> > >
> > > so the script crashes and there seems to be no error in the output
> file.
> > > I don't know where I am committing mistake.
> > > kindly help me out
> > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > >
> >
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> > >
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> >
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Received on Mon Jul 11 2016 - 14:00:06 PDT
