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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】如何处理算不动的情况
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Prettyswan

木虫 (小有名气)

[交流] 【求助成功】如何处理算不动的情况

我计算BaFe2As2体系的掺杂的结构驰豫，80个原子，5×5×5的kmesh，结果算不动了。由于以前算过CaFe2As2的80个原子的掺杂，结构跟这个是一样的、参数也一样，就直接拿过来用了，本来以为没有问题的但是发现算不动了（集群仍然会失去响应，并且把进程杀死）。我top了一下
引用回帖:
top - 20:33:26 up 28 days,  4:15,  1 user,  load average: 1.62, 1.14, 1.04
Tasks:  83 total,   6 running,  76 sleeping,   0 stopped,   1 zombie
Cpu(s): 77.3% us, 22.5% sy,  0.0% ni,  0.0% id,  0.0% wa,  0.0% hi,  0.2% si
Mem:   4040672k total,  3542632k used,   498040k free,    15588k buffers
Swap:  2096472k total,    69036k used,  2027436k free,    41792k cached

我以为是内存不够了（占用了将近90%），根据说明书的《6.68   Not enough memory, what to do》修改了INCAR
引用回帖:
System = BaFe2As2 afm1-DopSe:3.125%
PREC = Accurate
ISPIN = 2
MAGMOM = 16*0 16*3 16*-3 32*0
ISMEAR = 1
SIGMA = 0.20
ISTART = 0
EDIFF = 1E-5
EDIFFG = -1E-3
ICHARG = 2
ENCUT = 310
NSW = 60
IBRION = 2
ISIF ＝ 3 #Full relaxtion
POTIM ＝ 0.2
LORBIT = 11

LREAL = Auto
LPLANE ＝ .TRUE.
LSCALU ＝ .FALSE.
LCHARG = .FALSE. #连同的LWAVE和ISYM都是根据说明书上的设置的
LWAVE = .FALSE.
ISYM = 0
NPAR ＝ 1
NSIM ＝ 4

结果发现还是不行，却好像不是内存不够，但是集群仍然会失去响应，并且把进程杀死
引用回帖:
top - 20:58:46 up 28 days,  4:40,  1 user,  load average: 4.42, 8.11, 6.55
Tasks:  83 total,   6 running,  76 sleeping,   0 stopped,   1 zombie
Cpu(s): 83.1% us, 16.8% sy,  0.0% ni,  0.0% id,  0.0% wa,  0.0% hi,  0.1% si
Mem:   4040672k total,  2679192k used,  1361480k free,     3856k buffers
Swap:  2096472k total,   109684k used,  1986788k free,    41344k cached

请问大家是如何应对算不动的情况的呢？kpoints
引用回帖:
Automatic generation
0
Monhkorst-Pack
5 5 5
0.0 0.0 0.0

poscar
引用回帖:
System = BaFe2As2 dopGe 3.125%
   1.00000000000000
       5.615874999999996       0.000000000000002      12.942809999999996
      -5.615874999999998       0.000000000000000      12.942809999999996
       0.000000000000001     -11.142509999999998       0.000000000000002
   16   32   1   31
Direct
     -0.0000000000000000   0.2499999999999999  -0.0000000000000000
     -0.0000000000000000   0.2499999999999999   0.4999999999999999
      0.0000000000000000   0.7499999999999998  -0.0000000000000000
      0.0000000000000000   0.7499999999999998   0.4999999999999999
      0.4999999999999999   0.2499999999999999   0.0000000000000000
      0.4999999999999999   0.2500000000000000   0.4999999999999999
      0.4999999999999999   0.7499999999999999  -0.0000000000000000
      0.4999999999999998   0.7499999999999998   0.4999999999999999
      0.2499999999999999  -0.0000000000000000   0.2499999999999999
      0.2500000000000000  -0.0000000000000000   0.7499999999999999
      0.2499999999999999   0.4999999999999999   0.2499999999999999
      0.2499999999999999   0.4999999999999999   0.7499999999999999
      0.7499999999999999  -0.0000000000000000   0.2499999999999999
      0.7499999999999999   0.0000000000000001   0.7499999999999998
      0.7499999999999999   0.4999999999999998   0.2499999999999999
      0.7500000000000001   0.5000000000000001   0.7499999999999998
      0.0000000000000001   0.0000000000000000   0.1249999999999999
      0.0000000000000000   0.0000000000000000   0.6249999999999998
      0.0000000000000000   0.4999999999999999   0.1249999999999999
      0.0000000000000000   0.4999999999999998   0.6249999999999998
      0.5000000000000000  -0.0000000000000000   0.1249999999999999
      0.5000000000000000  -0.0000000000000001   0.6249999999999998
      0.4999999999999999   0.4999999999999999   0.1249999999999999
      0.0000000000000000  -0.0000000000000000   0.3749999999999999
     -0.0000000000000000   0.0000000000000000   0.8749999999999999
      0.0000000000000000   0.4999999999999999   0.3749999999999999
     -0.0000000000000000   0.4999999999999999   0.8749999999999999
      0.4999999999999999  -0.0000000000000000   0.3749999999999999
      0.4999999999999999  -0.0000000000000001   0.8749999999999998
      0.4999999999999998   0.4999999999999998   0.3749999999999999
      0.4999999999999999   0.4999999999999997   0.8749999999999998
      0.2499999999999999   0.2500000000000000   0.3749999999999999 #-3
      0.2500000000000000   0.2499999999999999   0.8749999999999997 #-3
      0.2500000000000000   0.7499999999999998   0.3749999999999999 #-3
      0.2500000000000000   0.7499999999999998   0.8749999999999997 #-3
      0.7499999999999999   0.2500000000000000   0.3749999999999999 #-3
      0.7499999999999999   0.2500000000000000   0.8750000000000000 #-3
      0.7499999999999998   0.7499999999999998   0.3749999999999999 #-3
      0.7499999999999999   0.7499999999999999   0.8750000000000000 #-3
      0.2500000000000000   0.2499999999999999   0.1249999999999999 #-3
      0.2499999999999999   0.2499999999999999   0.6249999999999998 #-3
      0.2499999999999999   0.7499999999999998   0.1249999999999999 #-3
      0.2499999999999999   0.7499999999999998   0.6249999999999998 #-3
      0.7499999999999998   0.2499999999999999   0.1249999999999999 #-3
      0.7499999999999999   0.2499999999999998   0.6249999999999998 #-3
      0.7500000000000000   0.7499999999999999   0.1249999999999999 #-3
      0.7499999999999999   0.7499999999999999   0.6249999999999998 #-3
      0.4999999999999999   0.4999999999999999   0.6249999999999998 #dopSe
      0.1770334988832470   0.4270334988832471  -0.0000000000000001
      0.1770334988832470   0.4270334988832472   0.4999999999999999
      0.1770334988832470   0.9270334988832469  -0.0000000000000001
      0.1770334988832471   0.9270334988832470   0.4999999999999999
      0.6770334988832470   0.4270334988832472  -0.0000000000000001
      0.6770334988832469   0.4270334988832471   0.4999999999999999
      0.6770334988832470   0.9270334988832470  -0.0000000000000001
      0.6770334988832468   0.9270334988832469   0.4999999999999999
      0.3229665011167530   0.0729665011167528  -0.0000000000000001
      0.3229665011167529   0.0729665011167528   0.4999999999999998
      0.3229665011167529   0.5729665011167526  -0.0000000000000001
      0.3229665011167529   0.5729665011167525   0.4999999999999998
      0.8229665011167527   0.0729665011167527  -0.0000000000000001
      0.8229665011167527   0.0729665011167527   0.4999999999999998
      0.8229665011167529   0.5729665011167527  -0.0000000000000001
      0.8229665011167527   0.5729665011167527   0.4999999999999998
      0.4270334988832472   0.1770334988832471   0.2500000000000000
      0.4270334988832472   0.1770334988832470   0.7499999999999999
      0.4270334988832472   0.6770334988832469   0.2500000000000000
      0.4270334988832471   0.6770334988832469   0.7499999999999999
      0.9270334988832472   0.1770334988832470   0.2500000000000000
      0.9270334988832470   0.1770334988832471   0.7500000000000000
      0.9270334988832472   0.6770334988832469   0.2500000000000000
      0.9270334988832472   0.6770334988832469   0.7500000000000000
      0.0729665011167528   0.3229665011167529   0.2500000000000001
      0.0729665011167528   0.3229665011167529   0.7500000000000000
      0.0729665011167527   0.8229665011167527   0.2500000000000001
      0.0729665011167527   0.8229665011167527   0.7500000000000000
      0.5729665011167527   0.3229665011167529   0.2500000000000001
      0.5729665011167527   0.3229665011167529   0.7500000000000001
      0.5729665011167527   0.8229665011167527   0.2500000000000001
      0.5729665011167529   0.8229665011167527   0.7500000000000001

[ Last edited by Prettyswan on 2010-11-16 at 17:45 ]
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1楼 2010-11-10 21:52:54
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Prettyswan

木虫 (小有名气)
引用回帖:
Originally posted by hedaors at 2010-11-10 22:55:58:
Ba 的原子要比 Ca 的多很多，内存就可能不够。
这个在要求精度不变的情况下，只能牺牲速度，你用的是几个核心？你只用一个核心提交任务试试，应该没问题。

我使用两个进程提交任务，提示虚拟内存不足；使用了一个进程进行计算，发现计算会很快退出并提示段错误，不管是并行（使用IFC）还是串行（使用gfortran）
引用回帖:
running on    1 nodes
distr:  one band on    1 nodes,    1 groups
vasp.4.6.28 25Jul05 complex
POSCAR found :  4 types and   80 ions
LDA part: xc-table for Pade appr. of Perdew
POSCAR, INCAR and KPOINTS ok, starting setup
WARNING: wrap around errors must be expected
[node11:02919] *** Process received signal ***
[node11:02919] Signal: Segmentation fault (11)
[node11:02919] Signal code: Address not mapped (1)
[node11:02919] Failing at address: 0x351761ab8
[node11:02919] [ 0] /lib64/tls/libpthread.so.0 [0x317210c430]
[node11:02919] [ 1] /home/software/openmpi-1.2.2-intel9/lib/libopen-pal.so.0 [0x2a966ea7f0]
[node11:02919] [ 2] /home/software/openmpi-1.2.2-intel9/lib/libopen-pal.so.0(_int_malloc+0x627) [0x2a966ea07f]
[node11:02919] [ 3] /home/software/openmpi-1.2.2-intel9/lib/libopen-pal.so.0(malloc+0x67) [0x2a966e93bf]
[node11:02919] [ 4] /home/bin/vasp.openmpi(for_allocate+0x89) [0x699c01]
[node11:02919] [ 5] /home/bin/vasp.openmpi(wave_mp_allocw_+0x2c7) [0x4a9977]
[node11:02919] [ 6] /home/bin/vasp.openmpi(MAIN__+0x1504d) [0x428b8d]
[node11:02919] [ 7] /home/bin/vasp.openmpi(main+0x32) [0x413b2a]
[node11:02919] [ 8] /lib64/tls/libc.so.6(__libc_start_main+0xdb) [0x317161c3fb]
[node11:02919] [ 9] /home/bin/vasp.openmpi [0x413a6a]
[node11:02919] *** End of error message ***
mpirun noticed that job rank 0 with PID 2919 on node node11 exited on signal 11 (Segmentation fault).

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6楼2010-11-11 08:59:12
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hedaors

禁虫 (正式写手)
★ ★
cenwanglai(金币+2):谢谢回复！ 2010-11-10 23:08:21
Prettyswan(金币+2): 2010-11-11 15:06:46
Ba 的原子要比 Ca 的多很多，内存就可能不够。
这个在要求精度不变的情况下，只能牺牲速度，你用的是几个核心？你只用一个核心提交任务试试，应该没问题。
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2楼2010-11-10 22:55:58
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bingmou

金虫 (著名写手)
★
sunyang1988(金币+1):谢谢交流 2010-11-10 23:50:22
Prettyswan(金币+1): 2010-11-11 15:08:09
对于80个原子这么多的体系，我的建议是K点取为1 1 1就可以了
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3楼2010-11-10 23:42:35
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Prettyswan

木虫 (小有名气)
引用回帖:
Originally posted by bingmou at 2010-11-10 23:42:35:
对于80个原子这么多的体系，我的建议是K点取为1 1 1就可以了

对于Monhkorst-Pack来说，它的最小k点为4，我使用3 3 3的kmesh都会提示出错。要想使用1 1 1就不能使用Monhkorst-Pack，要使用Gamma了。
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4楼2010-11-11 08:21:11
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