Re: RE: FATAL ERROR with "File exists"

From: Zhang Yan (yanzhang_at_moon.ibp.ac.cn)
Date: Thu Jan 17 2019 - 21:16:17 CST

I checked the version I used, It was the version NAMD_2.10_Linux-x86_64-multicore. Now I changed it to NAMD_2.13_Linux-x86_64-netlrts, the same problems occurs. Would you please tell which is the right mpi version?
On the other hand, I’m not clear what’s the difference between charmrun and mpirun, and when I need to use charmrun and under what condition I need to use mpirun. Sorry about the naive question. Hope I can solve my problem according to your help and explanation.

Regards,
Yan

> 在 2019年1月18日,上午2:36,Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov> 写道:
>
> Whenever I see mpi being invoked and things taking longer than they should, my first question is always what version of NAMD are you running? See my response below. Its also considered bad form to hijack threads. Electrons are free(ish)! Make your own thread please.
>
> -Josh
>
>
> On 2019-01-16 20:10:47-07:00 owner-namd-l_at_ks.uiuc.edu wrote:
>
> Hi,
> I’m using MDFF to make flexible fitting of the X-ray coordinate to my EM map. The sample has helical symmetry. So I make the namd configure with helical symmetry constrains. But after I submit my job, it looks like the computers have been keeping at the "Info: CREATING 48136 COMPUTE OBJECTS " stage for several days without no more new output. Why the processors can't go to the next computation stage, my system is too big? Any suggestions are appreciated.
> Regards,
> Yan
> The following is the last several lines of the log file after I submit my namd job, which always stay at this stage and no more lines are output:
> Info: Startup phase 5 took 4.29153e-05 s, 289.473 MB of memory in use
> Info: PATCH GRID IS 28 BY 25 BY 4
> Info: PATCH GRID IS 1-AWAY BY 1-AWAY BY 1-AWAY
> Info: REMOVING COM VELOCITY 0.00757615 0.0131683 0.0256697
> Info: LARGEST PATCH (10) HAS 1641 ATOMS
> Info: TORUS A SIZE 1 USING 0
> Info: TORUS B SIZE 1 USING 0
> Info: TORUS C SIZE 1 USING 0
> Info: TORUS MINIMAL MESH SIZE IS 1 BY 1 BY 1
> Info: Placed 100% of base nodes on same physical node as patch
> Info: Startup phase 6 took 0.162006 s, 323.578 MB of memory in use
> Info: Startup phase 7 took 0.000121117 s, 323.578 MB of memory in use
> Info: Startup phase 8 took 7.70092e-05 s, 323.578 MB of memory in use
> LDB: Central LB being created...
> Info: Startup phase 9 took 0.00112295 s, 323.578 MB of memory in use
> Info: CREATING 48136 COMPUTE OBJECTS
> Info: PATCH GRID IS 28 BY 25 BY 4
> Info: PATCH GRID IS 1-AWAY BY 1-AWAY BY 1-AWAY
> Info: REMOVING COM VELOCITY 0.00757615 0.0131683 0.0256697
> Info: LARGEST PATCH (10) HAS 1641 ATOMS
> Info: TORUS A SIZE 1 USING 0
> Info: TORUS B SIZE 1 USING 0
> Info: TORUS C SIZE 1 USING 0
> Info: TORUS MINIMAL MESH SIZE IS 1 BY 1 BY 1
> Info: Placed 100% of base nodes on same physical node as patch
> Info: Startup phase 6 took 0.162988 s, 323.578 MB of memory in use
> Info: Startup phase 7 took 0.000114918 s, 323.578 MB of memory in use
> Info: Startup phase 8 took 8.60691e-05 s, 323.578 MB of memory in use
> LDB: Central LB being created...
> Info: Startup phase 9 took 0.00116205 s, 323.578 MB of memory in use
> Info: CREATING 48136 COMPUTE OBJECTS
> The following is my job script:
> #!/bin/bash
> ### Inherit all current environment variables
> #PBS -V
> ### Job name
> #PBS -N 43nm
> ### Keep Output and Error
> #PBS -k eo
> ### Queue name
> #PBS -q quick
> ### Specify the number of nodes and thread (ppn) for your job.
> #PBS -l nodes=14:ppn=20
> #################################
> ### Switch to the working directory;
> cd $PBS_O_WORKDIR
> #Environment
> source ~/.bashrc
> NP=`echo 20 14 | gawk '//{print $1*$2}'`
> ###Run:
> echo "starting mdff..."
> #charmrun namd2 +p $NP 9-step1.namd > test.log
> mpirun --bynode -np $NP namd2 9-step1.namd > test.log
> echo "done"
> The following is my namd2 configure file:
> ### Docking -- Step 1
> set PSFFILE 9_autopsf.psf
> set PDBFILE 9_autopsf.pdb
> set GRIDPDB 9-grid.pdb
> set GBISON 0
> set DIEL 80
> set SCALING_1_4 1.0
> set ITEMP 300
> set FTEMP 300
> set GRIDFILE 43nm-grid.dx
> set GSCALE 6
> set EXTRAB {9-extrabonds.txt 9-extrabonds-cispeptide.txt 9-extrabonds-chirality.txt}
> set CONSPDB 0
> set FIXPDB 0
> set GRIDON 1
> set OUTPUTNAME 9-step1
> set TS 100000
> set MS 2000
> set MARGIN 0
> ####################################
> symmetryRestraints on
> symmetryfile helix-symmetry.pdb
> symmetryk 20
> symmetryMatrixFile matrix.txt
> symmetryfirststep 2001
> symmetryfirstfullstep 102000
> ####################################
> structure $PSFFILE
> coordinates $PDBFILE
> paraTypeCharmm on
> parameters par_all36_prot.prm
> if {[info exists INPUTNAME]} {
> BinVelocities $INPUTNAME.restart.vel
> BinCoordinates $INPUTNAME.restart.coor
> } else {
> temperature $ITEMP
> }
>
> 张艳
> Yan Zhang,
> Associate Professor,
> Institute of Biophysics,
> Chinese Academy of Sciences
>
>

张艳
Yan Zhang,
Associate Professor,
Institute of Biophysics,
Chinese Academy of Sciences

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