From NWChem
Viewed 905 times, With a total of 2 Posts
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Just Got Here
Threads 3
Posts 4
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| 3:19:59 PM PST - Mon, Feb 2nd 2015 |
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Hi all,
In the past NWChem worked well on my cluster, but recently it doesn't run as I expect given that I put a very simple input for it to run, and all of the sudden the supposed calculation did not start. I am very puzzled as to what actually happened and why doesn't it work.
Following is my .nw input file (named MP2_run1.nw). The MP2-01.xyz file exists in the same directory as the .nw file and the submission script.
title "HCl+4H2O SIP Form MP2/cc-pVTZ Optimization Run #1"
scratch_dir ./scratch
permanent_dir ./perm
charge 0
start HCl4H2O_MP2CCPVTZ_R01
geometry units angstrom noautosym noautoz
load format xyz MP2-01.xyz
end
basis
* library cc-pVTZ
end
driver
xyz HCl4H2O_SIP_MP2CCPVTZ_run01
maxiter 20
end
task mp2 optimize
Here is the submission script (the cluster is SGE-based).
#!/bin/bash
### SGE job parameters
#$ -N HCl4Wat_MP2CCPVTZ_MP2_1
#$ -q batch.q
#$ -l h_rt=20:00:00
#$ -pe orte 60
#$ -cwd
#$ -j y
#$ -S /bin/bash
#$ -V
#$ -M myemail@someinstitution.edu
### BEGIN timestamp
echo ""
echo -n "BEGIN: "
date
echo ""
### Program Execution
workDir=/home/my_username/optimization/HCl4Wat/SIP/temp
mpirun -np 60 nwchem-6.5 $workDir/MP2_run1.nw > $workDir/MP2_run1.out
### END timestamp
echo ""
echo -n "END: "
date
NWChem output gave me the following (it didn't even give the database file corresponding to the "start" directive in the permanent directory as stated in the input file)
Job information
---------------
hostname = compute-0-53.local
program = nwchem-6.5
date = Mon Feb 2 15:12:03 2015
compiled = Tue_Jan_20_21:30:05_2015
source = /home/wpornpat/NWChem-6.5
nwchem branch = 6.5
nwchem revision = 26243
ga revision = 10506
input = /home/wpornpat/PTime_Khun/optimization/HCl4Wat/SIP/temp/MP2_run1.nw
prefix = MP2_run1.
data base = ./MP2_run1.db
status = startup
nproc = 60
time left = -1s
Memory information
------------------
heap = 13107198 doubles = 100.0 Mbytes
stack = 13107195 doubles = 100.0 Mbytes
global = 26214400 doubles = 200.0 Mbytes (distinct from heap & stack)
total = 52428793 doubles = 400.0 Mbytes
verify = yes
hardfail = no
Directory information
---------------------
0 permanent = .
0 scratch = .
NWChem Input Module
-------------------
Summary of allocated global arrays
-----------------------------------
No active global arrays
GA Statistics for process 0
------------------------------
create destroy get put acc scatter gather read&inc
calls: 0 0 0 0 0 0 0 0
number of processes/call 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00
bytes total: 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00
bytes remote: 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00
Max memory consumed for GA by this process: 0 bytes
MA_summarize_allocated_blocks: starting scan ...
MA_summarize_allocated_blocks: scan completed: 0 heap blocks, 0 stack blocks
MA usage statistics:
allocation statistics:
heap stack
---- -----
current number of blocks 0 0
maximum number of blocks 0 0
current total bytes 0 0
maximum total bytes 0 0
maximum total K-bytes 0 0
maximum total M-bytes 0 0
It did not do anything at all, and immediately after that part of the output was the citation and running time summary. Could you please give me some suggestions as to what might happen or what do I need to do to fix this? Thank you.
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Edoapra Forum:Admin, Forum:Mod, bureaucrat, sysop
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Forum Vet
Threads 6
Posts 1014
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| 9:24:33 AM PST - Tue, Feb 3rd 2015 |
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"#" sign in title
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Khun Wasut
The "#" in the title string is causing the NWChem input file to ignore the rest of the input file.
How to fix:
Either replace "#" with something else or put the backslash "\" sign just before it, e.g.
"HCl+4H2O SIP Form MP2/cc-pVTZ Optimization Run \#1"
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Just Got Here
Threads 3
Posts 4
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| 9:46:13 AM PST - Tue, Feb 3rd 2015 |
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Edoapra,
Thank you so much! I went so far to recompile the whole thing but didn't realize that the problem is just escaping the character in the title.
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