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relion无法提交任务的解决方法  

2013-08-30 20:19:13|  分类: 默认分类 |  标签: |举报 |字号 订阅

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1. mpiexec: error while loading shared libraries: libtorque.so.2: cannot open shared object file: No such file or directory
解决方法:
(bash)在~/.bashrc下将 LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH添加进去
export PATH=/public/CBIshare/Software/workshop_soft/relion-1.2/bin:$PATH
export LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH
export PATH=/public/CBIshare/Software/workshop_soft/relion-1.2:$PATH
export RELION_QSUB_TEMPLATE="/public/CBIshare/Software/workshop_soft/relion-1.2/qsub.csh"
export RELION_CTFFIND3_EXECUTABLE="/public/CBIshare/Software/workshop_soft/ctffind3.exe"
export PATH=/usr/local/bin:$PATH

(csh)
setenv LD_LIBRARY_PATH /usr/local/lib:$LD_LIBRARY_PATH

2.[node2:24085] [[64770,1],0] ORTE_ERROR_LOG: Data unpack would read past end of buffer in file util/nidmap.c at line 118
[node2:24085] [[64770,1],0] ORTE_ERROR_LOG: Data unpack would read past end of buffer in file ess_env_module.c at line 174
--------------------------------------------------------------------------
It looks like orte_init failed for some reason; your parallel process is
likely to abort.  There are many reasons that a parallel process can
fail during orte_init; some of which are due to configuration or
environment problems.  This failure appears to be an internal failure;
here's some additional information (which may only be relevant to an
Open MPI developer):

  orte_util_nidmap_init failed
解决方法:mpi在bash下正常,但再csh下不正常,貌似解决方法是将一些路径添加到~/.cshrc中,记不清了

3. /var/spool/torque/mom_priv/jobs/271.emcluster.cbi.ibp.ac.cn.SC: line 12: /usr/local/bin/mpiexec: No such file or directory
解决方法:
(1)在各个节点上安装openmpi。
(2)在公共节点上安装openmpi,然后写到各节点的目录中。

4。  === MPI setup ===
 + Number of MPI processes            = 8
 + Master  (0) runs on host            = node2
 + Slave     1 runs on host            = node2
 + Slave     2 runs on host            = node2
 + Slave     3 runs on host            = node2
 + Slave     4 runs on host            = node2
 + Slave     5 runs on host            = node2
 + Slave     6 runs on host            = node2
 + Slave     7 runs on host            = node2
 =================
 Using CTFFINDs executable in: /public/CBIshare/Software/workshop_soft/ctffind3.exe
 to estimate CTF parameters for the following micrographs:
 Extract particles based on the following (boxer) coordinate files:
 Estimating CTF parameters using CTFFIND3 ...
 Extracting particles from the micrographs ...
 Joining all metadata in one STAR file...
 Written out STAR file with all particles in particles.star
 Done!
解决方法:
没有报错,但啥都没有。原来再relion里头要填写绝对路径:
input micrographs: /sugon/CBI/DingWei/set_002_challenge_2/Micrographs/*.mrc
Particle coordinate files: /sugon/CBI/DingWei/set_002_challenge_2/Micrographs/*.box
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