在旧群集中使用Slurm（和PBS）的Oneapi的Mpirun错误
最近，我安装了Intel Oneapi，包括C编译器，Fortran编译器和MPI库，并遵守了VASP。
在提出问题之前，我需要在安装VASP时需要澄清一些技巧：
- Glibc2.14：群集是一台具有GLIBC版本2.12的旧机器，其中Oneapi需要2.14版。因此，我编译了glibc2.14并导出ld_path：
导出ld_library_path =“〜/mySoft/mysoft/glibc214/lib：$ ld_library_path” - ld 2.24：群集，虽然需要更高的版本。因此，我安装了Binutils 2.24。
有一台主计算机与群集中的30个计算节点相连。计算以3种方式执行：
- 当我在主中进行计算时，完全可以。
- 当我用
rsh命令手动登录节点时，登录节点中的计算也没有问题。 - 但是通常我从主（带有slurm或pbs）提交计算脚本，然后在节点中进行计算。在那种情况下，我遇到了以下错误消息：
[[email protected]] poll_for_event (../../../../../src/pm/i_hydra/libhydra/demux/hydra_demux_poll.c:159): check exit codes error
[[email protected]] HYD_dmx_poll_wait_for_proxy_event (../../../../../src/pm/i_hydra/libhydra/demux/hydra_demux_poll.c:212): poll for event error
[[email protected]] HYD_bstrap_setup (../../../../../src/pm/i_hydra/libhydra/bstrap/src/intel/i_hydra_bstrap.c:1062): error waiting for event
[[email protected]] HYD_print_bstrap_setup_error_message (../../../../../src/pm/i_hydra/mpiexec/intel/i_mpiexec.c:1015): error setting up the bootstrap proxies
[[email protected]] Possible reasons:
[[email protected]] 1. Host is unavailable. Please check that all hosts are available.
[[email protected]] 2. Cannot launch hydra_bstrap_proxy or it crashed on one of the hosts. Make sure hydra_bstrap_proxy is available on all hosts and it has right permissions.
[[email protected]] 3. Firewall refused connection. Check that enough ports are allowed in the firewall and specify them with the I_MPI_PORT_RANGE variable.
[[email protected]] 4. pbs bootstrap cannot launch processes on remote host. You may try using -bootstrap option to select alternative launcher.
我只通过ONEAPI编译的代码遇到了此错误，但Intel®Parallel Studio XE已编译。您对这个错误有任何想法吗？您的回应将不胜感激。
最好，
莱昂
Recently I installed Intel OneAPI including c compiler, FORTRAN compiler and mpi library and complied VASP with it.
Before presenting the question, there are some tricks I need to clarify during the installation of VASP:
- GLIBC2.14: the cluster is an old machine with a glibc version of 2.12, where OneAPI needs a version of 2.14. So I compile the GLIBC2.14 and export the ld_path:
export LD_LIBRARY_PATH="~/mysoft/glibc214/lib:$LD_LIBRARY_PATH" - ld 2.24: The
ldversion is 2.20 in the cluster, while a higher version is needed. So I installed binutils 2.24.
There is one master computer connected with 30 calculating nodes in the cluster. The calculation is executed with 3 ways:
- When I do the calculation in the master, it's totally OK.
- When I login the nodes manually with
rshcommand, the calculation in the logged node is also no problem. - But usually I submit the calculation script from the master (with slurm or pbs), and then do the calculation in the node. In that case, I met following error message:
[[email protected]] poll_for_event (../../../../../src/pm/i_hydra/libhydra/demux/hydra_demux_poll.c:159): check exit codes error
[[email protected]] HYD_dmx_poll_wait_for_proxy_event (../../../../../src/pm/i_hydra/libhydra/demux/hydra_demux_poll.c:212): poll for event error
[[email protected]] HYD_bstrap_setup (../../../../../src/pm/i_hydra/libhydra/bstrap/src/intel/i_hydra_bstrap.c:1062): error waiting for event
[[email protected]] HYD_print_bstrap_setup_error_message (../../../../../src/pm/i_hydra/mpiexec/intel/i_mpiexec.c:1015): error setting up the bootstrap proxies
[[email protected]] Possible reasons:
[[email protected]] 1. Host is unavailable. Please check that all hosts are available.
[[email protected]] 2. Cannot launch hydra_bstrap_proxy or it crashed on one of the hosts. Make sure hydra_bstrap_proxy is available on all hosts and it has right permissions.
[[email protected]] 3. Firewall refused connection. Check that enough ports are allowed in the firewall and specify them with the I_MPI_PORT_RANGE variable.
[[email protected]] 4. pbs bootstrap cannot launch processes on remote host. You may try using -bootstrap option to select alternative launcher.
I only met this error with oneAPI compiled codes but Intel® Parallel Studio XE compiled. Do you have any idea of this error? Your response will be highly appreciated.
Best,
Léon
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可能是权限错误，而Slurm代理没有正确的权限或库路径？
Could it be a permissions error with the Slurm agent not having the correct permissions or library path?