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gleerat

木虫 (正式写手)

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专业: 凝聚态物性 II ：电子结构

[交流] 【求助成功】VASP运行错误已有3人参与

今天集群上的VASP出问题了，请大家看看是什么问题。谢谢了

引用回帖:

running on 4 nodes
distr: one band on 1 nodes, 4 groups
vasp.4.6.28 25Jul05 complex
POSCAR found : 0 types and 0 ions
[node5:25238] *** Process received signal ***
[node5:25238] Signal: Segmentation fault (11)
[node5:25238] Signal code: Address not mapped (1)
[node5:25238] Failing at address: 0x100
[node5:25238] [ 0] /lib64/tls/libpthread.so.0 [0x30bc30c430]
[node5:25238] [ 1] /home/bin/vasp.openmpi(cvt_text_to_ieee_t+0x44) [0x6b8e7c]
[node5:25238] [ 2] /home/bin/vasp.openmpi(for__cvt_value+0xa4c) [0x6b53a2]
[node5:25238] [ 3] /home/bin/vasp.openmpi(for_read_int_lis_xmit+0x6c6) [0x6928dc]
[node5:25238] [ 4] /home/bin/vasp.openmpi(rdatab_+0x143c) [0x6734b0]
[node5:25238] [ 5] /home/bin/vasp.openmpi(reader_+0x4f93) [0x5d364b]
[node5:25238] [ 6] /home/bin/vasp.openmpi(MAIN__+0x27c6) [0x416306]
[node5:25238] [ 7] /home/bin/vasp.openmpi(main+0x32) [0x413b2a]
[node5:25238] [ 8] /lib64/tls/libc.so.6(__libc_start_main+0xdb) [0x30bb81c3fb]
[node5:25238] [ 9] /home/bin/vasp.openmpi [0x413a6a]
[node5:25238] *** End of error message ***
[node5:25240] *** Process received signal ***
[node5:25240] Signal: Segmentation fault (11)
[node5:25240] Signal code: Address not mapped (1)
[node5:25240] Failing at address: 0x100
[node5:25240] [ 0] /lib64/tls/libpthread.so.0 [0x30bc30c430]
[node5:25240] [ 1] /home/bin/vasp.openmpi(cvt_text_to_ieee_t+0x44) [0x6b8e7c]
[node5:25240] [ 2] /home/bin/vasp.openmpi(for__cvt_value+0xa4c) [0x6b53a2]
[node5:25240] [ 3] /home/bin/vasp.openmpi(for_read_int_lis_xmit+0x6c6) [0x6928dc]
[node5:25240] [ 4] /home/bin/vasp.openmpi(rdatab_+0x143c) [0x6734b0]
[node5:25240] [ 5] /home/bin/vasp.openmpi(reader_+0x4f93) [0x5d364b]
[node5:25240] [ 6] /home/bin/vasp.openmpi(MAIN__+0x27c6) [0x416306]
[node5:25240] [ 7] /home/bin/vasp.openmpi(main+0x32) [0x413b2a]
[node5:25240] [ 8] /lib64/tls/libc.so.6(__libc_start_main+0xdb) [0x30bb81c3fb]
[node5:25240] [ 9] /home/bin/vasp.openmpi [0x413a6a]
[node5:25240] *** End of error message ***
[node5:25239] *** Process received signal ***
[node5:25239] Signal: Segmentation fault (11)
[node5:25239] Signal code: Address not mapped (1)
[node5:25239] Failing at address: 0x100
[node5:25239] [ 0] /lib64/tls/libpthread.so.0 [0x30bc30c430]
[node5:25239] [ 1] /home/bin/vasp.openmpi(cvt_text_to_ieee_t+0x44) [0x6b8e7c]
[node5:25239] [ 2] /home/bin/vasp.openmpi(for__cvt_value+0xa4c) [0x6b53a2]
[node5:25239] [ 3] /home/bin/vasp.openmpi(for_read_int_lis_xmit+0x6c6) [0x6928dc]
[node5:25239] [ 4] /home/bin/vasp.openmpi(rdatab_+0x143c) [0x6734b0]
[node5:25239] [ 5] /home/bin/vasp.openmpi(reader_+0x4f93) [0x5d364b]
[node5:25239] [ 6] /home/bin/vasp.openmpi(MAIN__+0x27c6) [0x416306]
[node5:25239] [ 7] /home/bin/vasp.openmpi(main+0x32) [0x413b2a]
[node5:25239] [ 8] /lib64/tls/libc.so.6(__libc_start_main+0xdb) [0x30bb81c3fb]
[node5:25239] [ 9] /home/bin/vasp.openmpi [0x413a6a]
[node5:25239] *** End of error message ***
[node5:25237] *** Process received signal ***
[node5:25237] Signal: Segmentation fault (11)
[node5:25237] Signal code: Address not mapped (1)
[node5:25237] Failing at address: 0x100
[node5:25237] [ 0] /lib64/tls/libpthread.so.0 [0x30bc30c430]
[node5:25237] [ 1] /home/bin/vasp.openmpi(cvt_text_to_ieee_t+0x44) [0x6b8e7c]
[node5:25237] [ 2] /home/bin/vasp.openmpi(for__cvt_value+0xa4c) [0x6b53a2]
[node5:25237] [ 3] /home/bin/vasp.openmpi(for_read_int_lis_xmit+0x6c6) [0x6928dc]
[node5:25237] [ 4] /home/bin/vasp.openmpi(rdatab_+0x143c) [0x6734b0]
[node5:25237] [ 5] /home/bin/vasp.openmpi(reader_+0x4f93) [0x5d364b]
[node5:25237] [ 6] /home/bin/vasp.openmpi(MAIN__+0x27c6) [0x416306]
[node5:25237] [ 7] /home/bin/vasp.openmpi(main+0x32) [0x413b2a]
[node5:25237] [ 8] /lib64/tls/libc.so.6(__libc_start_main+0xdb) [0x30bb81c3fb]
[node5:25237] [ 9] /home/bin/vasp.openmpi [0x413a6a]
[node5:25237] *** End of error message ***
mpirun noticed that job rank 0 with PID 25237 on node node5 exited on signal 11 (Segmentation fault).
3 additional processes aborted (not shown)

后来我发现，vasp本身没问题，是我使用的一个脚本，之前这个脚本一直正常的，现在脚本出问题了。命令放在脚本中就会出错。

引用回帖:

#!/bin/sh
rm WAVECAR
for i in 0.95 0.96 0.97 0.98 0.99 1.00
do
cat > POSCAR < System = CaFe2As2 afm-opt
  0.96999999999999997
$i 0.0000000000000000 0.0000000000000000
   0.0000000000000000 5.4501999999999997 0.0000000000000000
   0.0000000000000000 0.0000000000000000 5.5061999999999998
4 8 8
Direct
  0.0000000000000000 -0.0000000000000000 -0.0000000000000000
  0.0000000000000000  0.5000000000000000  0.5000000000000000
  0.5000000000000000 -0.0000000000000000  0.5000000000000000
  0.5000000000000000  0.5000000000000000 -0.0000000000000000
  0.2500000000000000  0.2500000000000000  0.2500000000000000
  0.7500000000000000  0.7500000000000000  0.2500000000000000
  0.7500000000000000  0.2500000000000000  0.7500000000000000
  0.2500000000000000  0.7500000000000000  0.7500000000000000
  0.7500000000000000  0.7500000000000000  0.7500000000000000
  0.7500000000000000  0.2500000000000000  0.2500000000000000
  0.2500000000000000  0.7500000000000000  0.2500000000000000
  0.2500000000000000  0.2500000000000000  0.7500000000000000
  0.3608571367508424  0.0000000000000000  0.0000000000000000
  0.3608571367508424  0.5000000000000000  0.5000000000000000
  0.8608571367508423 -0.0000000000000000  0.5000000000000000
  0.8608571367508423  0.5000000000000000  0.0000000000000000
  0.6391428632491577 -0.0000000000000000  0.0000000000000000
  0.6391428632491577  0.5000000000000000  0.5000000000000000
  0.1391428632491576  0.0000000000000000  0.5000000000000000
  0.1391428632491576  0.5000000000000000  0.0000000000000000
!
cp INCAR.relax INCAR ; cp KPOINTS.relax KPOINTS
echo "c= $i Full Relaxtion"
/home/software/openmpi-1.2.2-intel9/bin/mpirun -np 4 /home/bin/vasp.openmpi
cp OUTCAR OUTCAR.relax ; cp OSZICAR OSZICAR.relax
cp CONTCAR POSCAR ; cp INCAR.static INCAR ; cp KPOINTS.static KPOINTS
echo "c= $i Static Selfconsistent"
/home/software/openmpi-1.2.2-intel9/bin/mpirun -np 4 /home/bin/vasp.openmpi
cp OSZICAR OSZICAR.static ; cp OUTCAR OUTCAR.static
cp INCAR.nsc INCAR ; cp KPOINTS.nsc KPOINTS
echo "c= $i Non-Selfconsistent"
/home/software/openmpi-1.2.2-intel9/bin/mpirun -np 4 /home/bin/vasp.openmpi
cp OUTCAR "c=$i_OUTCAR"
E=`grep "TOTEN" OUTCAR | tail -1 | awk '{printf "%12.6f \n", $5 }'`
V=`grep "volume" OUTCAR | tail -1 | awk '{printf "%12.4f \n", $5 }'`
echo $i $V $E >>EtVo.dat
echo $i $E >>murn.in
done

[ Last edited by gleerat on 2010-11-13 at 13:07 ]

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