numpy仅通过LSF导入SystemError和segfault（OpenBLAS blas_thread_init：pthread_create：资源暂时不可用）

时间：2018-07-04 18:14:39

标签： python numpy lsf openblas

当我在通过LSF运行的脚本中导入带有blas 1.1的numpy时，在重复'Boundary of string'和OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable的实例之后，它会出现SystemError和分段错误。当我在LSF之外的相同环境下的同一台计算机上运行相同的脚本时，它将成功。它还在blas 1.0（在LSF内部或外部）成功。

我按以下方式运行OpenBLAS blas_thread_init: RLIMIT_NPROC 1032189 current, 1032189 max：

bsub

bsub -q short-serial -W 00:01 -R "rusage[mem=1000]" -M 1000 -cwd $HOME -oo ~/test.lsf.out -eo ~/test.lsf.err -J test $HOME/test.sh 是包装程序，以确保我在干净的环境中运行test.sh，以确保无论在LSF内部还是外部运行，情况都相同：

test2.sh

在$ cat test.sh #!/bin/sh env -i ~/test2.sh --noprofile --norc 中，我写出并设置了一些环境信息，然后运行Python尝试进行test2.sh：

import numpy

通过LSF运行此命令将产生以下标准输出：

$ cat test2.sh
export
ulimit -a
ldconfig -v
export PATH=
.  /group_workspaces/cems2/fiduceo/Users/gholl/anaconda3/etc/profile.d/conda.sh
conda activate
conda activate FCDR
python -c "import numpy; print('Success 1')"
python ~/mwe.py

（为简洁起见，省略了$ cat test.lsf.out Sender: LSF System <lsfadmin@host334.jc.rl.ac.uk> Subject: Job 2475445: <test> in cluster <lotus> Exited Job <test> was submitted from host <host293.jc.rl.ac.uk> by user <gholl> in cluster <lotus> at Wed Jul 4 18:44:42 2018. Job was executed on host(s) <host334.jc.rl.ac.uk>, in queue <short-serial>, as user <gholl> in cluster <lotus> at Wed Jul 4 18:44:42 2018. </home/users/gholl> was used as the home directory. </home/users/gholl> was used as the working directory. Started at Wed Jul 4 18:44:42 2018. Terminated at Wed Jul 4 18:44:44 2018. Results reported at Wed Jul 4 18:44:44 2018. Your job looked like: ------------------------------------------------------------ # LSBATCH: User input /home/users/gholl/test.sh ------------------------------------------------------------ Exited with exit code 139. Resource usage summary: CPU time : 0.60 sec. Max Memory : - Average Memory : - Total Requested Memory : 1000.00 MB Delta Memory : - Max Swap : - Max Processes : - Max Threads : - Run time : 2 sec. Turnaround time : 2 sec. The output (if any) follows: export OLDPWD export PWD="/home/users/gholl" export SHLVL="1" core file size (blocks, -c) unlimited data seg size (kbytes, -d) unlimited scheduling priority (-e) 0 file size (blocks, -f) unlimited pending signals (-i) 1032189 max locked memory (kbytes, -l) unlimited max memory size (kbytes, -m) unlimited open files (-n) 4096 pipe size (512 bytes, -p) 8 POSIX message queues (bytes, -q) 819200 real-time priority (-r) 0 stack size (kbytes, -s) 8589930496 cpu time (seconds, -t) unlimited max user processes (-u) 1032189 virtual memory (kbytes, -v) unlimited file locks (-x) unlimited 的输出）

ldconfig -v

然后到stderr：

PS:

Read file </home/users/gholl/test.lsf.err> for stderr output of this job.

我也研究了$ cat test.lsf.err /sbin/ldconfig: /etc/ld.so.conf.d/kernel-2.6.32-696.23.1.el6.x86_64.conf:6: duplicate hwcap 1 nosegneg /sbin/ldconfig: /etc/ld.so.conf.d/kernel-2.6.32-754.el6.x86_64.conf:6: duplicate hwcap 1 nosegneg /sbin/ldconfig: /opt/platform_mpi/lib/linux_amd64/libhpmpi.so is not an ELF file - it has the wrong magic bytes at the start. /sbin/ldconfig: Can't create temporary cache file /etc/ld.so.cache~: Permission denied OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable OpenBLAS blas_thread_init: RLIMIT_NPROC 1032189 current, 1032189 max OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable OpenBLAS blas_thread_init: RLIMIT_NPROC 1032189 current, 1032189 max OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable OpenBLAS blas_thread_init: RLIMIT_NPROC 1032189 current, 1032189 max OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable OpenBLAS blas_thread_init: RLIMIT_NPROC 1032189 current, 1032189 max OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable OpenBLAS blas_thread_init: RLIMIT_NPROC 1032189 current, 1032189 max OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable OpenBLAS blas_thread_init: RLIMIT_NPROC 1032189 current, 1032189 max OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable OpenBLAS blas_thread_init: RLIMIT_NPROC 1032189 current, 1032189 max OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable OpenBLAS blas_thread_init: RLIMIT_NPROC 1032189 current, 1032189 max OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable OpenBLAS blas_thread_init: RLIMIT_NPROC 1032189 current, 1032189 max OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable OpenBLAS blas_thread_init: RLIMIT_NPROC 1032189 current, 1032189 max OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable OpenBLAS blas_thread_init: RLIMIT_NPROC 1032189 current, 1032189 max OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable OpenBLAS blas_thread_init: RLIMIT_NPROC 1032189 current, 1032189 max OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable OpenBLAS blas_thread_init: RLIMIT_NPROC 1032189 current, 1032189 max OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable OpenBLAS blas_thread_init: RLIMIT_NPROC 1032189 current, 1032189 max OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable OpenBLAS blas_thread_init: RLIMIT_NPROC 1032189 current, 1032189 max OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable OpenBLAS blas_thread_init: RLIMIT_NPROC 1032189 current, 1032189 max OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable OpenBLAS blas_thread_init: RLIMIT_NPROC 1032189 current, 1032189 max OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable OpenBLAS blas_thread_init: RLIMIT_NPROC 1032189 current, 1032189 max OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable OpenBLAS blas_thread_init: RLIMIT_NPROC 1032189 current, 1032189 max Traceback (most recent call last): File "<string>", line 1, in <module> File "/group_workspaces/cems2/fiduceo/Users/gholl/anaconda3/envs/FCDR/lib/python3.6/site-packages/numpy/__init__.py", line 142, in <module> from . import add_newdocs File "/group_workspaces/cems2/fiduceo/Users/gholl/anaconda3/envs/FCDR/lib/python3.6/site-packages/numpy/add_newdocs.py", line 13, in <module> from numpy.lib import add_newdoc File "/group_workspaces/cems2/fiduceo/Users/gholl/anaconda3/envs/FCDR/lib/python3.6/site-packages/numpy/lib/__init__.py", line 8, in <module> from .type_check import * File "/group_workspaces/cems2/fiduceo/Users/gholl/anaconda3/envs/FCDR/lib/python3.6/site-packages/numpy/lib/type_check.py", line 11, in <module> import numpy.core.numeric as _nx File "/group_workspaces/cems2/fiduceo/Users/gholl/anaconda3/envs/FCDR/lib/python3.6/site-packages/numpy/core/__init__.py", line 16, in <module> from . import multiarray SystemError: initialization of multiarray raised unreported exception /home/users/gholl/test2.sh: line 8: 52786 Segmentation fault (core dumped) python -c "import numpy; print('Success 1')" OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable OpenBLAS blas_thread_init: RLIMIT_NPROC 1032189 current, 1032189 max OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable OpenBLAS blas_thread_init: RLIMIT_NPROC 1032189 current, 1032189 max OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable OpenBLAS blas_thread_init: RLIMIT_NPROC 1032189 current, 1032189 max OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable OpenBLAS blas_thread_init: RLIMIT_NPROC 1032189 current, 1032189 max OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable OpenBLAS blas_thread_init: RLIMIT_NPROC 1032189 current, 1032189 max OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable OpenBLAS blas_thread_init: RLIMIT_NPROC 1032189 current, 1032189 max OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable OpenBLAS blas_thread_init: RLIMIT_NPROC 1032189 current, 1032189 max OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable OpenBLAS blas_thread_init: RLIMIT_NPROC 1032189 current, 1032189 max OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable OpenBLAS blas_thread_init: RLIMIT_NPROC 1032189 current, 1032189 max OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable OpenBLAS blas_thread_init: RLIMIT_NPROC 1032189 current, 1032189 max OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable OpenBLAS blas_thread_init: RLIMIT_NPROC 1032189 current, 1032189 max OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable OpenBLAS blas_thread_init: RLIMIT_NPROC 1032189 current, 1032189 max OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable OpenBLAS blas_thread_init: RLIMIT_NPROC 1032189 current, 1032189 max OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable OpenBLAS blas_thread_init: RLIMIT_NPROC 1032189 current, 1032189 max OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable OpenBLAS blas_thread_init: RLIMIT_NPROC 1032189 current, 1032189 max OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable OpenBLAS blas_thread_init: RLIMIT_NPROC 1032189 current, 1032189 max OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable OpenBLAS blas_thread_init: RLIMIT_NPROC 1032189 current, 1032189 max OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable OpenBLAS blas_thread_init: RLIMIT_NPROC 1032189 current, 1032189 max OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable OpenBLAS blas_thread_init: RLIMIT_NPROC 1032189 current, 1032189 max Traceback (most recent call last): File "/home/users/gholl/mwe.py", line 2, in <module> import numpy File "/group_workspaces/cems2/fiduceo/Users/gholl/anaconda3/envs/FCDR/lib/python3.6/site-packages/numpy/__init__.py", line 142, in <module> from . import add_newdocs File "/group_workspaces/cems2/fiduceo/Users/gholl/anaconda3/envs/FCDR/lib/python3.6/site-packages/numpy/add_newdocs.py", line 13, in <module> from numpy.lib import add_newdoc File "/group_workspaces/cems2/fiduceo/Users/gholl/anaconda3/envs/FCDR/lib/python3.6/site-packages/numpy/lib/__init__.py", line 8, in <module> from .type_check import * File "/group_workspaces/cems2/fiduceo/Users/gholl/anaconda3/envs/FCDR/lib/python3.6/site-packages/numpy/lib/type_check.py", line 11, in <module> import numpy.core.numeric as _nx File "/group_workspaces/cems2/fiduceo/Users/gholl/anaconda3/envs/FCDR/lib/python3.6/site-packages/numpy/core/__init__.py", line 16, in <module> from . import multiarray SystemError: initialization of multiarray raised unreported exception /home/users/gholl/test2.sh: line 9: 52789 Segmentation fault (core dumped) python ~/mwe.py 的输出，但是我不知道要寻找什么，放置到这里太久了。但是，是否通过LSF运行时，我确实比较了排序后的输出：

ldconfig -v

当我在LSF之外跑步时，标准输出是

$ diff -u <(sort test.lsf.out_core) <(sort test.nolsf.out_core)
--- /dev/fd/63  2018-07-04 18:56:05.405440986 +0100
+++ /dev/fd/62  2018-07-04 18:56:05.405440986 +0100
@@ -1,4 +1,4 @@
-core file size          (blocks, -c) unlimited
+core file size          (blocks, -c) 0
 cpu time               (seconds, -t) unlimited
 data seg size           (kbytes, -d) unlimited
 export OLDPWD
@@ -102,9 +102,12 @@
        libBrokenLocale.so.1 -> libBrokenLocale-2.12.so
        libBrokenLocale.so.1 -> libBrokenLocale-2.12.so
        libbtf.so.1 -> libbtf.so.1.1.0
+       libbtparser.so.2 -> libbtparser.so.2.2.2
        libbz2.so.1 -> libbz2.so.1.0.4
        libcairo.so.2 -> libcairo.so.2.10800.8
        libcamd.so.2 -> libcamd.so.2.2.0
+       libcanberra-gtk.so.0 -> libcanberra-gtk.so.0.1.5
+       libcanberra.so.0 -> libcanberra.so.0.2.1
        libcanna16.so.1 -> libcanna16.so.1.2.0
        libcanna.so.1 -> libcanna.so.1.2.0
        libcap-ng.so.0 -> libcap-ng.so.0.0.0
@@ -116,7 +119,7 @@
        libcdt.so.5 -> libcdt.so.5.0.0
        libcfitsio.so.0 -> libcfitsio.so.0
        libcgraph.so.6 -> libcgraph.so.6.0.0
-       libcgroup.so.1 -> libcgroup.so.1.0.40
+       libCharLS.so.1 -> libCharLS.so.1.0
        libcholmod.so.1 -> libcholmod.so.1.7.1
        libcidn.so.1 -> libcidn-2.12.so
        libcidn.so.1 -> libcidn-2.12.so
@@ -188,6 +191,7 @@
        libeggdbus-1.so.0 -> libeggdbus-1.so.0.0.0
        libEGL.so.1 -> libEGL.so.1.0.0
        libelf.so.1 -> libelf-0.164.so
+       libenchant.so.1 -> libenchant.so.1.5.0
        libepoxy.so.0 -> libepoxy.so.0.0.0
        libesoobS.so.2 -> libesoobS.so.2.0.0
        libevent-1.4.so.2 -> libevent-1.4.so.2.1.3
@@ -263,6 +267,7 @@
        libgmodule-2.0.so.0 -> libgmodule-2.0.so.0.2800.8
        libgmp.so.3 -> libgmp.so.3.5.0
        libgmpxx.so.4 -> libgmpxx.so.4.1.0
+       libgnomecanvas-2.so.0 -> libgnomecanvas-2.so.0.2600.0
        libgnutls-extra.so.26 -> libgnutls-extra.so.26.22.6
        libgnutls.so.26 -> libgnutls.so.26.22.6
        libgnutlsxx.so.26 -> libgnutlsxx.so.26.14.12
@@ -357,6 +362,7 @@
        libgstvideo-0.10.so.0 -> libgstvideo-0.10.so.0.20.0
        libgta.so.0 -> libgta.so.0.0.1
        libgthread-2.0.so.0 -> libgthread-2.0.so.0.2800.8
+       libgtksourceview-2.0.so.0 -> libgtksourceview-2.0.so.0.0.0
        libgtk-x11-2.0.so.0 -> libgtk-x11-2.0.so.0.2400.23
        libgtrtst.so.2 -> libgtrtst.so.2.0.0
        libgudev-1.0.so.0 -> libgudev-1.0.so.0.0.1
@@ -378,9 +384,9 @@
        libhwloc.so.4 -> libhwloc.so
 /lib/i686: (hwcap: 0x0008000000000000)
 /lib/i686/nosegneg: (hwcap: 0x0028000000000000)
-       libibmad.so.5 -> libibmad.so.5.4.0
+       libibmad.so.5 -> libibmad.so.5.5.0
        libibnetdisc.so.5 -> libibnetdisc.so.5.3.0
-       libibumad.so.3 -> libibumad.so.3.0.4
+       libibumad.so.3 -> libibumad.so.3.1.0
        libibverbs.so.1 -> libibverbs.so.1.0.0
        libICE.so.6 -> libICE.so.6.3.0
        libicudata.so.42 -> libicudata.so.42.1
@@ -499,6 +505,7 @@
        libnih.so.1 -> libnih.so.1.0.0
        libnl.so.1 -> libnl.so.1.1.4
        libnn.so.2 -> libnn.so.2.0.0
+       libnotify.so.1 -> libnotify.so.1.2.3
        libnsl.so.1 -> libnsl-2.12.so
        libnsl.so.1 -> libnsl-2.12.so
        libnspr4.so -> libnspr4.so
@@ -542,17 +549,17 @@
        libopcodes-2.20.51.0.2-5.48.el6.so -> libopcodes-2.20.51.0.2-5.48.el6.so
        libopenjp2.so.7 -> libopenjp2.so.2.3.0
        libopenjpeg.so.2 -> libopenjpeg.so.2.1.3.0
-       libopensm.so.5 -> libopensm.so.5.2.0
+       libopensm.so.12 -> libopensm.so.12.0.0
        liboplodbcS.so.2 -> liboplodbcS.so.2.0.0
        liboraodbcS.so.2 -> liboraodbcS.so.2.0.0
        libORBit-2.so.0 -> libORBit-2.so.0.1.0
        libORBitCosNaming-2.so.0 -> libORBitCosNaming-2.so.0.1.0
        libORBit-imodule-2.so.0 -> libORBit-imodule-2.so.0.0.0
-       libosmcomp.so.3 -> libosmcomp.so.3.0.8
+       libosmcomp.so.3 -> libosmcomp.so.3.0.6
        libOSMesa16.so.6 -> libOSMesa16.so.6.5.3
        libOSMesa32.so.6 -> libOSMesa32.so.6.5.3
        libOSMesa.so.6 -> libOSMesa.so.6.5.3
-       libosmvendor.so.3 -> libosmvendor.so.3.0.9
+       libosmvendor.so.3 -> libosmvendor.so.3.0.8
        libossp-uuid.so.16 -> libossp-uuid.so.16.0.21
        libotf.so.0 -> libotf.so.0.0.0
        libp11-kit.so.0 -> libp11-kit.so.0.0.0
@@ -676,7 +683,6 @@
        libsensors.so.4 -> libsensors.so.4.2.0
        libsepol.so.1 -> libsepol.so.1
        libserf-1.so.1 -> libserf-1.so.1.3.0
-       libsgutils2.so.2 -> libsgutils2.so.2.0.0
        libshiboken-python2.7.so.1.2 -> libshiboken-python2.7.so.1.2.1
        libshp.so.1 -> libshp.so.1.0.1
        libslang.so.2 -> libslang.so.2.2.1
@@ -686,6 +692,7 @@
        libsndfile.so.1 -> libsndfile.so.1.0.20
        libsnmp.so.20 -> libsnmp.so.20.0.0
        libsoftokn3.so -> libsoftokn3.so
+       libspatialite.so.2 -> libspatialite.so.2.0.4
        libspqr.so.1 -> libspqr.so.1.1.2
        libsqlite3.so.0 -> libsqlite3.so.0.8.6
        libssh2.so.1 -> libssh2.so.1.0.1
@@ -754,6 +761,7 @@
        libvorbisenc.so.2 -> libvorbisenc.so.2.0.6
        libvorbisfile.so.3 -> libvorbisfile.so.3.3.2
        libvorbis.so.0 -> libvorbis.so.0.4.3
+       libvpx.so.1 -> libvpx.so.1.3.0
        libvte.so.9 -> libvte.so.9.2501.0
        libwbclient.so.0 -> libwbclient.so.0
        libwebpdecoder.so.1 -> libwebpdecoder.so.1.0.3
@@ -764,6 +772,7 @@
        libwlm-nosched.so -> libwlm-nosched.so
        libwmf-0.2.so.7 -> libwmf-0.2.so.7.1.0
        libwmflite-0.2.so.7 -> libwmflite-0.2.so.7.0.1
+       libwnck-1.so.22 -> libwnck-1.so.22.3.23
        libwrap.so.0 -> libwrap.so.0.7.6
        libwx_baseu-2.8.so.0 -> libwx_baseu-2.8.so.0.8.0
        libwx_baseu-3.0.so.0 -> libwx_baseu-3.0.so.0.2.0
@@ -800,6 +809,7 @@
        libX11.so.6 -> libX11.so.6.3.0
        libX11-xcb.so.1 -> libX11-xcb.so.1.0.0
        libX11-xcb.so.1 -> libX11-xcb.so.1.0.0
+       libx86.so.1 -> libx86.so.1
        libXau.so.6 -> libXau.so.6.0.0
        libXau.so.6 -> libXau.so.6.0.0
        libXaw3d.so.7 -> libXaw3d.so.7.0
@@ -842,6 +852,7 @@
        libxcb.so.1 -> libxcb.so.1.1.0
        libxcb-sync.so.1 -> libxcb-sync.so.1.0.0
        libxcb-sync.so.1 -> libxcb-sync.so.1.0.0
+       libxcb-util.so.1 -> libxcb-util.so.1.0.0
        libxcb-xevie.so.0 -> libxcb-xevie.so.0.0.0
        libxcb-xevie.so.0 -> libxcb-xevie.so.0.0.0
        libxcb-xf86dri.so.0 -> libxcb-xf86dri.so.0.0.0
@@ -889,6 +900,7 @@
        libXp.so.6 -> libXp.so.6.2.0
        libXrandr.so.2 -> libXrandr.so.2.2.0
        libXrender.so.1 -> libXrender.so.1.3.0
+       libXRes.so.1 -> libXRes.so.1.0.0
        libxslt.so.1 -> libxslt.so.1.1.26
        libxtables.so.4 -> libxtables.so.4.0.0-1.4.7
        libXt.so.6 -> libXt.so.6.0.0
@@ -897,20 +909,21 @@
        libXxf86dga.so.1 -> libXxf86dga.so.1.0.0
        libXxf86misc.so.1 -> libXxf86misc.so.1.1.0
        libXxf86vm.so.1 -> libXxf86vm.so.1.0.0
-       libyaml-0.so.2 -> libyaml-0.so.2.0.4
        libz.so.1 -> libz.so.1.2.3
 max locked memory       (kbytes, -l) unlimited
 max memory size         (kbytes, -m) unlimited
-max user processes              (-u) 1032189
-open files                      (-n) 4096
+max user processes              (-u) 1024
+open files                      (-n) 48000
 /opt/platform_mpi/lib/linux_amd64:
        p11-kit-trust.so -> libnssckbi.so
-pending signals                 (-i) 1032189
+pending signals                 (-i) 515955
 pipe size            (512 bytes, -p) 8
 POSIX message queues     (bytes, -q) 819200
 real-time priority              (-r) 0
 scheduling priority             (-e) 0
-stack size              (kbytes, -s) 8589930496
+stack size              (kbytes, -s) 2097151
+Success
+Success 1
 /usr/lib:
 /usr/lib64:
 /usr/lib64/atlas:

（为简便起见，省略了$ env -i ~/test2.sh --noprofile --norc export OLDPWD export PWD="/home/users/gholl" export SHLVL="1" core file size (blocks, -c) 0 data seg size (kbytes, -d) unlimited scheduling priority (-e) 0 file size (blocks, -f) unlimited pending signals (-i) 515955 max locked memory (kbytes, -l) unlimited max memory size (kbytes, -m) unlimited open files (-n) 48000 pipe size (512 bytes, -p) 8 POSIX message queues (bytes, -q) 819200 real-time priority (-r) 0 stack size (kbytes, -s) 2097151 cpu time (seconds, -t) unlimited max user processes (-u) 1024 virtual memory (kbytes, -v) unlimited file locks (-x) unlimited 的输出）     成功1     成功

并且将stderr的输出限制为与以前相同的ldconfig错误：

ldconfig -v

我正在使用主要来自/sbin/ldconfig: /etc/ld.so.conf.d/kernel-2.6.32-696.23.1.el6.x86_64.conf:6: duplicate hwcap 1 nosegneg /sbin/ldconfig: /etc/ld.so.conf.d/kernel-2.6.32-754.el6.x86_64.conf:6: duplicate hwcap 1 nosegneg /sbin/ldconfig: /opt/platform_mpi/lib/linux_amd64/libhpmpi.so is not an ELF file - it has the wrong magic bytes at the start. /sbin/ldconfig: Can't create temporary cache file /etc/ld.so.cache~: Permission denied 和anaconda的conda环境运行Python 3.6.3。我注意到previously，当我设置严格的conda-forge时，ulimit -v会失败，并显示相同的import numpy。但是目前，没有OpenBLAS blas_thread_init: pthread_create: Resource temporarily unavailable设置。 LSF和非LSF情况之间的唯一ulimit -v区别在于，对于某些属性，LSF内的限制比LSF外的限制更为慷慨，因此我看不到ulimit限制如何导致LSF内的故障。这个案例。在我以前的案例中，我也设法在LSF之外重现该问题。

为什么我可以直接导入numpy，但是通过LSF运行numpy时会出现SystemError和分段错误？我应该怎么看才能进一步调试它？

我没有LSF管理员访问权限。

1 个答案:

答案 0 :(得分：0)

我不知道为什么，但是设置后一切运行正常

export OMP_NUM_THREADS=1
export USE_SIMPLE_THREADED_LEVEL3= 1
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