dd_short_gmx (beta) VERY short

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boboviz

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Message 4546 - Posted: 23 Dec 2016, 14:52:52 UTC

On my linux vm are 4 to 6 seconds for wu! :-O
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Sergey Kovalchuk

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Message 4551 - Posted: 29 Dec 2016, 14:40:07 UTC

'exec' bit for ./gmx ?

drwxrwx--x 6 boinc boinc 4096 Dec 29 16:31 .
drwxrwx--x 15 boinc boinc 4096 Dec 28 15:45 ..
-rwxrwxrwx 1 boinc boinc 138532 Dec 9 13:30 3uh4_complex.pdb
drwxrwxrwx 2 boinc boinc 4096 Dec 9 15:14 LIG2
drwxr-xr-x 2 boinc boinc 4096 Dec 29 16:31 LIG2_long_run
-rwxrwxrwx 1 boinc boinc 3780 Dec 29 13:58 atommass.dat
-rw-r--r-- 1 boinc boinc 0 Dec 29 16:31 boinc_lockfile
-rw-r--r-- 1 boinc boinc 8192 Dec 29 16:32 boinc_mmap_file
-rw-r--r-- 1 boinc boinc 4108 Dec 29 16:31 complex.pdb
-rw-r--r-- 1 boinc boinc 8800567 Dec 29 16:31 dd_short_gmx.in
-rwxr-xr-x 1 boinc boinc 221170 Dec 29 16:31 dd_short_gmx_600_x86_64-pc-linux-gnu
-rwxrwxrwx 1 boinc boinc 3940 Dec 29 13:58 elements.dat
-rw-r--r-- 1 boinc boinc 20068560 Dec 29 15:17 gmx
-rwxr-xr-x 1 boinc boinc 1945 Dec 29 14:30 gromacs_md_preparation_pdb.sh
-rw-r--r-- 1 boinc boinc 5220 Dec 29 16:31 init_data.xml
-rw-r--r-- 1 boinc boinc 89 Dec 29 16:31 job.xml
drwxrwxrwx 2 boinc boinc 4096 Dec 9 13:35 mdp_files
drwxrwxrwx 2 boinc boinc 4096 Dec 29 13:58 oplsaa.ff
-rw-r--r-- 1 boinc boinc 135999 Dec 29 16:31 protein.pdb
-rwxrwxrwx 1 boinc boinc 2691 Dec 29 13:58 residuetypes.dat
-rwxrwxrwx 1 boinc boinc 29266 Dec 29 13:58 spc216.gro
-rwxrwxrwx 1 boinc boinc 343 Dec 29 13:58 specbond.dat
-rw-r--r-- 1 boinc boinc 1948 Dec 29 16:31 stderr.txt
-rwxrwxrwx 1 boinc boinc 848 Dec 29 13:58 vdwradii.dat
-rwxrwxrwx 1 boinc boinc 681 Dec 29 13:58 xlateat.dat
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Profile Krzysztof Piszczek - wspieram Polski Projekt Boinc
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Message 4552 - Posted: 29 Dec 2016, 15:41:50 UTC - in response to Message 4551.  

Yes, we work on it, also on other bug.
Krzysztof 'krzyszp' Piszczek

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fzs600

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Message 4553 - Posted: 29 Dec 2016, 18:42:40 UTC - in response to Message 4552.  

29 Dec 2016, 18:34:09 UTC 29 Dec 2016, 18:39:18 UTC Error while computing 3.15 0.01 --- TEST dd_short_gmx v7.00
x86_64-pc-linux-gnu

29 Dec 2016, 18:34:09 UTC 29 Dec 2016, 18:39:18 UTC Error while computing 1.15 0.01 --- TEST dd_short_gmx v7.00
x86_64-pc-linux-gnu
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Sergey Kovalchuk

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Message 4554 - Posted: 30 Dec 2016, 8:03:32 UTC

library versions mismatch on Ubuntu 14.04

./gmx: /usr/lib/x86_64-linux-gnu/libgomp.so.1: version `GOMP_4.0' not found (required by ./gmx)
./gmx: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.20' not found (required by ./gmx)


I installed GROMACS from OS distribution. Can I switch application to a local binary?

Similar difficulties have been with the project BURP. There you can switch to the local blender using file "native" in the project folder
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Message 4556 - Posted: 30 Dec 2016, 16:40:32 UTC - in response to Message 4554.  

If you have installed Gromacs 5.4.1 then yes but other versions are incompatible.
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Message 4558 - Posted: 2 Jan 2017, 11:22:57 UTC

In a case if WU falls immediately on you system you need to install two library packages:
libblas3
liblapack3
Krzysztof 'krzyszp' Piszczek

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Profile Maurice Goulois

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Message 4559 - Posted: 2 Jan 2017, 11:47:14 UTC

Looking at failed wu results, installed missing libs :) waiting for next wu
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Sergey Kovalchuk

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Message 4560 - Posted: 2 Jan 2017, 12:01:26 UTC - in response to Message 4558.  
Last modified: 2 Jan 2017, 12:47:02 UTC

In a case if WU falls immediately on you system you need to install two library packages:
libblas3
liblapack3


I have already been installed. And a package 'gromacs' with all dependencies, but old version 4.6.5 from OS distro :-(
All WU with eror:
./gmx: /usr/lib/x86_64-linux-gnu/libgomp.so.1: version `GOMP_4.0' not found (required by ./gmx)
./gmx: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.20' not found (required by ./gmx)


[edit]
after "apt-get install zip unzip" - task ~20 sec but validated with warning
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Sergey Kovalchuk

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Message 4562 - Posted: 2 Jan 2017, 12:53:04 UTC

Start job on Ubuntu 16.04 - host
Got a normal output from application, but an error "exceeded elapsed time limit 498.39 (1000000.00G/2006.46G)"
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Message 4570 - Posted: 4 Jan 2017, 22:17:54 UTC - in response to Message 4562.  

Yes, we know the problem.
Basically, every WU is really a set of shell commands. In some cases, some commands execute before previous one finish. It should not happens but... it happens. We work hardly to find a on solution.
Just for explanation, wrapper do script like (or similar) to this one:
#!/bin/bash

source /usr/local/gromacs/bin/GMXRC
cp LIG7/LIG7_GMX.itp ./LIG7.itp

#grep LIG 3uh4_complex.pdb > LIG.pdb
grep ATOM 3uh4_complex.pdb > protein.pdb

./gmx pdb2gmx -f protein.pdb -o protein_processed.pdb -p topol.top -water tip3p <<EOF
5
EOF

grep -h ATOM protein_processed.pdb ./LIG7/LIG7_NEW.pdb > complex.pdb

./gmx editconf -f complex.pdb -o newbox.pdb -c -d 1.2 -bt dodecahedron
# topology edition1
sed -i '/Protein             1/a LIG7                1' topol.top
sed -i '/\#include \".*\.ff\/forcefield.itp\"/a \#include \"LIG7.itp\"' topol.top

# solvation
./gmx solvate -cp newbox.pdb -cs spc216.gro -p topol.top -o solv.pdb
./gmx grompp -f ./mdp_files/em.mdp -c solv.pdb -p topol.top -o ions.tpr
./gmx genion -s ions.tpr -o solv_ions.pdb -p topol.top -neutral -conc 0.15<<EOF
15
EOF

# energy minimization
./gmx grompp -f ./mdp_files/em_real.mdp -c solv_ions.pdb -p topol.top -o em.tpr
./gmx mdrun -v -deffnm em   #dluuuuuugie

# remove pbc artefacts
./gmx trjconv -s em.tpr -f em.gro -o em_1.gro -pbc nojump <<EOF
0
EOF

./gmx genrestr -f ./LIG7/LIG7_NEW.pdb -o posre_LIG.itp -fc 1000 1000 1000 <<EOF
2
EOF
# topology edition2
sed -i '/\; Include water topology/i \; Ligand position restraints\n\#ifdef POSRES\n\#include \"posre_LIG\.itp\"\n\#endif\n' topol.top

./gmx make_ndx -f em_1.gro -o index.ndx <<EOF
1 | 13
q
EOF
./gmx grompp -f ./mdp_files/nvt.mdp -c em_1.gro -p topol.top -n index.ndx -o nvt.tpr
./gmx mdrun -deffnm nvt
./gmx grompp -f ./mdp_files/npt.mdp -c nvt.gro -t nvt.cpt -p topol.top -n index.ndx -o npt.tpr
./gmx mdrun -deffnm npt
./gmx grompp -f ./mdp_files/md.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o md_0_1.tpr
./gmx mdrun -nt 1 -deffnm md_0_1


And somewhere in line 10 SOMETIMES misses order... we work to find why...
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Message boards : Number crunching : dd_short_gmx (beta) VERY short


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