[molpro-user] test job hangs on FC2 Xeon Node
Dr Seth OLSEN
s.olsen1 at uq.edu.au
Tue Nov 23 06:16:54 GMT 2004
Hello Molpro-Users,
As outlined in previous communiques, I have been having no luck in getting molpro2002.6 to run on a Dual Xeon node with Fedora Core 2, either as the installed rpm or as a self-compiled version done with ifc7 or ifc8. The problem is as follows. After the integral sort, the process writes no more to output but becomes unkillable with 99.9%CPU and 1.0%Mem as given by 'top'.
In order to help diagnose the problem, I have turned the 'gprint,io,cpu' directive on in a given failing job (bccd_opt.test). The following are the last lines written to output for that job with the io printing turned on:
EXTENDING RECORD 1300.1 BY 34949. WORDS TO 38820. IMPLEMENTATION=df EXTENSION 0
NUMBER OF SORTED TWO-ELECTRON INTEGRALS: 34949. BUFFER LENGTH: 32768
NUMBER OF SEGMENTS: 1 SEGMENT LENGTH: 34949 RECORD LENGTH: 524288
Memory used in sort: 0.59 MW
OPENW FILE 24 NAME=/scratch/root/eaf_T2400002627.TMP IMPLEMENTATION=eaf STATUS=scratch HANDLE= 2
OPEN EAF FILE 24 NAME= IMPLEMENTATION=eaf
CLOSEW FILE 21 NAME=eaf_T2100002627.TMP IMPLEMENTATION=eaf HANDLE= 1
CLOSE EAF FILE 21
To determine what files might be opened by molpro at the time that the program stops functioning, I issue a 'lsof | grep molpro' command while the program is running in it's 'unkillable' final status. The following is the output of that command:
bash 2210 root cwd DIR 8,1 12288 295282 /opt/molpro/testjobs
molpro 2624 root cwd DIR 8,2 4096 2796193 /scratch/root
molpro 2624 root rtd DIR 8,1 4096 2 /
molpro 2624 root txt REG 8,1 41552 491923 /usr/local/lib/molpro-mpp-Linux-i686-i4-2002.6/molpro
molpro 2624 root mem REG 8,1 1455084 82119 /lib/tls/libc-2.3.3.so
molpro 2624 root mem REG 8,1 106892 375519 /lib/ld-2.3.3.so
molpro 2624 root 0u CHR 136,1 3 /dev/pts/1
molpro 2624 root 1u CHR 136,1 3 /dev/pts/1
molpro 2624 root 2u CHR 136,1 3 /dev/pts/1
molpro 2624 root 4u REG 8,1 823 18013 /tmp/tmpfuX2LXr (deleted)
parallel 2626 root txt REG 8,1 30180 491926 /usr/local/lib/molpro-mpp-Linux-i686-i4-2002.6/parallel
parallel 2626 root 1u REG 8,1 12113 295235 /opt/molpro/testjobs/bccd_opt.out
molprop_2 2627 root cwd DIR 8,2 4096 2796193 /scratch/root
molprop_2 2627 root rtd DIR 8,1 4096 2 /
molprop_2 2627 root txt REG 8,1 19346064 491925 /usr/local/lib/molpro-mpp-Linux-i686-i4-2002.6/molprop_2002_6_p4_tcgmsg.exe
molprop_2 2627 root mem REG 8,1 96248 375542 /lib/libnsl-2.3.3.so
molprop_2 2627 root mem REG 8,1 106892 375519 /lib/ld-2.3.3.so
molprop_2 2627 root mem REG 8,1 1455084 82119 /lib/tls/libc-2.3.3.so
molprop_2 2627 root mem REG 8,1 214796 82121 /lib/tls/libm-2.3.3.so
molprop_2 2627 root mem REG 8,1 43528 375552 /lib/libnss_nis-2.3.3.so
molprop_2 2627 root mem REG 8,1 50944 375549 /lib/libnss_files-2.3.3.so
molprop_2 2627 root 0u REG 8,1 823 18013 /tmp/tmpfuX2LXr (deleted)
molprop_2 2627 root 1u REG 8,1 12113 295235 /opt/molpro/testjobs/bccd_opt.out
molprop_2 2627 root 2u CHR 136,1 3 /dev/pts/1
molprop_2 2627 root 3u IPv4 4464 TCP sphinx128.giza:32846->sphinx128.giza:32844 (ESTABLISHED)
molprop_2 2627 root 4u REG 8,1 1457 18014 /tmp/forttempG1uyhO
molprop_2 2627 root 5u REG 8,1 74 18015 /tmp/forttempfYdJb0
molprop_2 2627 root 6u REG 8,1 0 18016 /tmp/forttemp2hFU5b
molprop_2 2627 root 7u REG 8,1 0 18017 /tmp/forttemp9p96Zn
molprop_2 2627 root 8u REG 8,2 3006888 2796194 /scratch/root/df_T0100002627.TMP (deleted)
molprop_2 2627 root 9u REG 8,2 182344 2796195 /scratch/root/df_T0200002627.TMP (deleted)
molprop_2 2627 root 10u REG 8,2 182344 2796196 /scratch/root/df_T0300002627.TMP (deleted)
molprop_2 2627 root 11u REG 8,2 0 2796197 /scratch/root/df_T0400002627.TMP (deleted)
molprop_2 2627 root 12r REG 8,1 476967 491914 /usr/local/lib/molpro-mpp-Linux-i686-i4-2002.6/libmol.index
molprop_2 2627 root 13u REG 8,2 3428352 2796199 /scratch/root/eaf_T2400002627.TMP (deleted)
So, it appears that the *.TMP files that molpro has most recently opened and closed are listed as deleted but still open. I cannot find these files in the specified directory, which makes sense if they are deleted, but if they are deleted than how can they be currently open files?
Cheers,
Seth Olsen
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Dr Seth Olsen, PhD
Postdoctoral Fellow, Computational Systems Biology Group
Centre for Computational Molecular Science
Chemistry Building,
The University of Queensland
Qld 4072, Brisbane, Australia
tel (617) 33653732
fax (617) 33654623
email: s.olsen1 at uq.edu.au
Web: www.ccms.uq.edu.au
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