我一直在努力让并行HDF5在群集上工作一整周但没有任何进展。我希望有人能帮助我。谢谢！
我正在使用RedHat Enterprise Linux 5.5 x86_64操作系统在光泽文件系统上构建Parallel HDF5（hdf5-1.8.15-patch1）。我试图用impi 4.0.2和openmpi 1.8编译它，它成功没有任何错误。当我“检查”时，他们都通过了串行测试，但在进入并行测试后立即挂起（特别是t_mpi）。最终，我不得不用ctrl + C来结束它。这是输出：
lijm@c01b03:~/yuan/hdf5-1.8.15-patch1/testpar$ make check
CC t_mpi.o
t_mpi.c: In function ‘test_mpio_gb_file’:
t_mpi.c:284: warning: passing argument 1 of ‘malloc’ with different width due to prototype
t_mpi.c:284: warning: request for implicit conversion from ‘void *’ to ‘char *’ not permitted in C++
t_mpi.c: In function ‘test_mpio_1wMr’:
t_mpi.c:465: warning: passing argument 2 of ‘gethostname’ with different width due to prototype
t_mpi.c: In function ‘test_mpio_derived_dtype’:
t_mpi.c:682: warning: declaration of ‘nerrors’ shadows a global declaration
t_mpi.c:37: warning: shadowed declaration is here
t_mpi.c:771: warning: passing argument 5 of ‘MPI_File_set_view’ discards qualifiers from pointer target type
t_mpi.c:798: warning: passing argument 2 of ‘MPI_File_set_view’ with different width due to prototype
t_mpi.c:798: warning: passing argument 5 of ‘MPI_File_set_view’ discards qualifiers from pointer target type
t_mpi.c:685: warning: unused variable ‘etypenew’
t_mpi.c:682: warning: unused variable ‘nerrors’
t_mpi.c: In function ‘main’:
t_mpi.c:1104: warning: too many arguments for format
t_mpi.c: In function ‘test_mpio_special_collective’:
t_mpi.c:991: warning: will never be executed
t_mpi.c:992: warning: will never be executed
t_mpi.c:995: warning: will never be executed
t_mpi.c: In function ‘test_mpio_gb_file’:
t_mpi.c:229: warning: will never be executed
t_mpi.c:232: warning: will never be executed
t_mpi.c:237: warning: will never be executed
t_mpi.c:238: warning: will never be executed
t_mpi.c:253: warning: will never be executed
t_mpi.c:258: warning: will never be executed
t_mpi.c:259: warning: will never be executed
t_mpi.c:281: warning: will never be executed
t_mpi.c:246: warning: will never be executed
t_mpi.c:267: warning: will never be executed
t_mpi.c:319: warning: will never be executed
t_mpi.c:343: warning: will never be executed
t_mpi.c:385: warning: will never be executed
t_mpi.c:389: warning: will never be executed
t_mpi.c:248: warning: will never be executed
t_mpi.c:269: warning: will never be executed
t_mpi.c: In function ‘main’:
t_mpi.c:1143: warning: will never be executed
t_mpi.c:88: warning: will never be executed
t_mpi.c:102: warning: will never be executed
t_mpi.c:133: warning: will never be executed
t_mpi.c:142: warning: will never be executed
CCLD t_mpi
make t_mpi testphdf5 t_cache t_pflush1 t_pflush2 t_pshutdown t_prestart t_shapesame
make[1]: Entering directory `/home/lijm/yuan/hdf5-1.8.15-patch1/testpar'
make[1]: `t_mpi' is up to date.
make[1]: `testphdf5' is up to date.
make[1]: `t_cache' is up to date.
make[1]: `t_pflush1' is up to date.
make[1]: `t_pflush2' is up to date.
make[1]: `t_pshutdown' is up to date.
make[1]: `t_prestart' is up to date.
make[1]: `t_shapesame' is up to date.
make[1]: Leaving directory `/home/lijm/yuan/hdf5-1.8.15-patch1/testpar'
make check-TESTS
make[1]: Entering directory `/home/lijm/yuan/hdf5-1.8.15-patch1/testpar'
make[2]: Entering directory `/home/lijm/yuan/hdf5-1.8.15-patch1/testpar'
make[3]: Entering directory `/home/lijm/yuan/hdf5-1.8.15-patch1/testpar'
make[3]: Nothing to be done for `_exec_check-s'.
make[3]: Leaving directory `/home/lijm/yuan/hdf5-1.8.15-patch1/testpar'
make[2]: Leaving directory `/home/lijm/yuan/hdf5-1.8.15-patch1/testpar'
make[2]: Entering directory `/home/lijm/yuan/hdf5-1.8.15-patch1/testpar'
===Parallel tests in testpar begin Thu Jun 11 22:07:48 CST 2015===
**** Hint ****
Parallel test files reside in the current directory by default.
Set HDF5_PARAPREFIX to use another directory. E.g.,
HDF5_PARAPREFIX=/PFS/user/me
export HDF5_PARAPREFIX
make check
**** end of Hint ****
make[3]: Entering directory `/home/lijm/yuan/hdf5-1.8.15-patch1/testpar'
============================
Testing t_mpi
============================
t_mpi Test Log
============================
===================================
MPI functionality tests
===================================
Proc 1: hostname=c01b03
Proc 2: hostname=c01b03
Proc 3: hostname=c01b03
Proc 5: hostname=c01b03
--------------------------------
Proc 0: *** MPIO 1 write Many read test...
--------------------------------
Proc 0: hostname=c01b03
Proc 4: hostname=c01b03
Command exited with non-zero status 255
0.08user 0.01system 0:37.65elapsed 0%CPU (0avgtext+0avgdata 0maxresident)k
0inputs+0outputs (0major+5987minor)pagefaults 0swaps
make[3]: *** [t_mpi.chkexe_] Error 1
make[2]: *** [build-check-p] Interrupt
make[1]: *** [test] Interrupt
make: *** [check-am] Interrupt
两个MPI实现的上述输出是相同的，但openmpi也输出警告：
警告：您的OpenFabrics子系统似乎配置为仅允许注册部分物理内存。这可能导致MPI作业以不稳定的性能，挂起和/或崩溃运行。
我已经搜索过这个问题了。但我不认为这可能是悬挂的原因，原因最后说明了。
我试图找到它挂起的地方。我发现它总是卡在它遇到的第一个集体功能上。例如，在t_mpi中。它首先挂在：
MPI_File_delete（filename，MPI_INFO_NULL）; （第477行），
在test_mpio_1wMr中。如果我注释掉这一行，它会被卡在MPI_File_open下方。但我不确定这些功能内部发生了什么。
我注意到了另一件事。我执行“make”的HDF5文件夹位于NFS文件系统中，我只能通过位于其他位置的特定文件夹访问光泽。所以，我发现如果我没有将HDF5_PARAPERFIX设置为我的lustre文件夹，测试运行得很好，因为默认情况下在本地执行测试。那么，我想它应该是与光泽本身有关的问题，而不是内存的限制？
谢谢！
答案 0 :(得分：0)
很难说这里发生了什么。
您可能正在申请＆＃34;通用unix文件系统＆＃34;对你的光彩推动者。英特尔MPI需要两个环境变量（I_MPI_EXTRA_FILESYSTEM和I_MPI_EXTRA_FILESYSTEM_LIST）才能使用优化光泽的代码路径:(有关详细信息，请参阅https://press3.mcs.anl.gov/romio/2014/06/12/romio-and-intel-mpi/）。
在构建OpenMPI时，您还必须明确请求光源支持。
如果您可以将调试器附加到一个或多个卡住的进程以查看其挂起的位置，那将会有很大帮助。卡在一个i / o例程上？陷入沟通？