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小木虫论坛-学术科研互动平台 » 计算模拟区 » 第一性原理 » Vasp&MedeA » 【求助成功】VASP运行错误
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gleerat

木虫 (正式写手)

[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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明察、慎思、笃行
1楼 2010-10-03 16:49:47
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bingmou

金虫 (著名写手)
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小木虫(金币+0.5):给个红包，谢谢回帖交流
cenwanglai(金币+1):呵呵，有啥办法呢？ 2010-10-07 11:19:42
段错误，明显是程序编译有错或者硬件有错
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2楼2010-10-03 17:08:20
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sunyang1988

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小木虫(金币+0.5):给个红包，谢谢回帖交流
bingmou(金币+2):应该是这个问题才对，谢谢交流 2010-10-03 22:05:03
POSCAR found :  0 types and    0 ions
POSCAR设置有问题吧
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心之所向无惧无悔
3楼2010-10-03 19:25:01
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gleerat

木虫 (正式写手)
★
zxzj05(金币+1):谢谢交流！ 2010-10-05 17:18:49
引用回帖:
Originally posted by bingmou at 2010-10-03 17:08:20:
段错误，明显是程序编译有错或者硬件有错

后来我才知道，软件没问题，直接用命令行执行vasp没问题，放在脚本中运行就出问题了。
奇怪的是这个脚本我用了很长时间了，一直没有出问题。这是我的脚本：
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
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明察、慎思、笃行
4楼2010-10-04 09:07:19
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bingmou

金虫 (著名写手)
★
小木虫(金币+0.5):给个红包，谢谢回帖交流
用这个脚本生成的POSCAR是怎么样的呢？
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5楼2010-10-05 09:54:29
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gleerat

木虫 (正式写手)
引用回帖:
Originally posted by bingmou at 2010-10-05 09:54:29:
用这个脚本生成的POSCAR是怎么样的呢？

应该是脚本中的i值取值过小（i值取错了，不是我的本意），我改变了i值之后就好了。
不过错误提示倒是很让人疑惑。
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明察、慎思、笃行
6楼2010-10-05 19:20:43
已阅   回复此楼   关注TA 给TA发消息 送TA红花 TA的回帖

bingmou

金虫 (著名写手)
★
小木虫(金币+0.5):给个红包，谢谢回帖交流
好吧，所以要看POSCAR之之前还要看看实验数据。计算不能离开数据
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7楼2010-10-05 20:05:59
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