Hi Jie, We can reproduce this issue here and will plan to fix it for the HDF5-1.10.2 release (Spring 2018).
-Barbara h...@hdfgroup.org From: Hdf-forum [mailto:hdf-forum-boun...@lists.hdfgroup.org] On Behalf Of ?? Sent: Friday, December 01, 2017 6:53 PM To: Scot Breitenfeld Cc: HDF Helpdesk; HDF Users Discussion List Subject: Re: [Hdf-forum] [SPAM] Errors when install HDF5 Hello, Scott: I run the command you said, and it doesn’t work: “ustc@USTC-PC:~$ mpiexec -n 6 t_mpi [proxy:0:0@USTC-PC] HYDU_create_process (../../utils/launch/launch.c:825): execvp error on file t_mpi (No such file or directory) [proxy:0:0@USTC-PC] HYDU_create_process (../../utils/launch/launch.c:825): execvp error on file t_mpi (No such file or directory) [proxy:0:0@USTC-PC] HYDU_create_process (../../utils/launch/launch.c:825): execvp error on file t_mpi (No such file or directory) [proxy:0:0@USTC-PC] HYDU_create_process (../../utils/launch/launch.c:825): execvp error on file t_mpi (No such file or directory) [proxy:0:0@USTC-PC] HYDU_create_process (../../utils/launch/launch.c:825): execvp error on file t_mpi (No such file or directory) [proxy:0:0@USTC-PC] HYDU_create_process (../../utils/launch/launch.c:825): execvp error on file t_mpi (No such file or directory)” How can I fix this problem? Best Regards Jie Jiang 在 2017年12月1日，下午11:53，Scot Breitenfeld <brtn...@hdfgroup.org<mailto:brtn...@hdfgroup.org>> 写道： Can you run the program “t_mpi” by itself and see if that works, mpiexec -n 6 t_mpi It looks like make check is only running with one process, which is controlled by the environment variable RUNPARALLEL, and I do see it is getting set correctly during build: RUNPARALLEL='mpiexec -n $${NPROCS:=6}' Scot On Dec 1, 2017, at 3:32 AM, 江捷 <jieji...@mail.ustc.edu.cn<mailto:jieji...@mail.ustc.edu.cn>> wrote: Hello, Scot: Thank you for your reply. I patch the Fortran source for Intel 18, and then configure with the command: "FC=/usr/local/bin/mpif90 ./configure --enable-parallel --prefix=/usr/local/hdf5 --enable-fortran --enable-shared" and then "make", no problem, but when I "make check", it has the followting errors: "Test if MPI_File_get_size works correctly with MPItest.h5 ***FAILED with 110592 total errors -------------------------------- Proc 0: *** MPIO independent overlapping writes... -------------------------------- Need at least 2 processes to run MPIO test. -SKIP- -------------------------------- Proc 0: *** MPIO complicated derived datatype test... -------------------------------- -------------------------------- Proc 0: *** MPIO special collective io test SKIPPED. -------------------------------- This test needs at least four processes to run. =================================== ***MPI tests detected 110592 errors*** =================================== Command exited with non-zero status 1 0.22user 0.11system 0:00.36elapsed 92%CPU (0avgtext+0avgdata 12560maxresident)k 0inputs+73960outputs (0major+19477minor)pagefaults 0swaps Makefile:1400: recipe for target 't_mpi.chkexe_' failed make[4]: *** [t_mpi.chkexe_] Error 1 make[4]: Leaving directory '/home/ustc/下载/hdf5-1.10.1/testpar' Makefile:1475: recipe for target 'build-check-p' failed make[3]: *** [build-check-p] Error 1 make[3]: Leaving directory '/home/ustc/下载/hdf5-1.10.1/testpar' Makefile:1380: recipe for target 'test' failed make[2]: *** [test] Error 2 make[2]: Leaving directory '/home/ustc/下载/hdf5-1.10.1/testpar' Makefile:1180: recipe for target 'check-am' failed make[1]: *** [check-am] Error 2 make[1]: Leaving directory '/home/ustc/下载/hdf5-1.10.1/testpar' Makefile:650: recipe for target 'check-recursive' failed make: *** [check-recursive] Error 1" I have attached the configure.out, make.out, check.out and config.log. Bests Regards Jie Jiang -----原始邮件----- 发件人:"Scot Breitenfeld" <brtn...@hdfgroup.org<mailto:brtn...@hdfgroup.org>> 发送时间:2017-11-30 23:09:16 (星期四) 收件人: "HDF Users Discussion List" <hdf-forum@lists.hdfgroup.org<mailto:hdf-forum@lists.hdfgroup.org>> 抄送: 主题: [SPAM] Re: [Hdf-forum] Errors when install HDF5 Did you patch the Fortran source for Intel 18? https://software.intel.com/en-us/forums/intel-fortran-compiler-for-linux-and-mac-os-x/topic/747951 Scot On Nov 30, 2017, at 8:13 AM, 江捷 <jieji...@mail.ustc.edu.cn<mailto:jieji...@mail.ustc.edu.cn>> wrote: Hello Barbara, Thank you for your reply. I reinstall my ifort2018 and read the readme carefully, change the figure line to the following two choices: "FC=/opt/intel/bin/ifort ./configure --prefix=/usr/local/hdf5 --enable-fortran" "FC=/usr/local/bin/mpif90 ./configure --enable-parallel --prefix=/usr/local/hdf5 --enable-fortran" and then "make", but both of them have the same error: "compilation aborted for H5f90global.F90 (code 1) Makefile:996: recipe for target 'H5f90global.lo' failed make[3]: *** [H5f90global.lo] Error 1 make[3]: Leaving directory '/home/ustc/Download/hdf5-1.10.1/fortran/src' Makefile:864: recipe for target 'all' failed make[2]: *** [all] Error 2 make[2]: Leaving directory '/home/ustc/Download/hdf5-1.10.1/fortran/src' Makefile:811: recipe for target 'all-recursive' failed make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory '/home/ustc/Download/hdf5-1.10.1/fortran' Makefile:650: recipe for target 'all-recursive' failed make: *** [all-recursive] Error 1" I have already add: "source /opt/intel/compilers_and_libraries_2018.1.163/linux/bin/compilervars.sh intel64" "export LD_LIBRARY_PATH=/usr/local/hdf5:${LD_LIBRARY_PATH}" to my .bashrc Best Regards, Jie -----原始邮件----- 发件人:"Barbara Jones" <bljo...@hdfgroup.org<mailto:bljo...@hdfgroup.org>> 发送时间:2017-11-20 23:36:39 (星期一) 收件人: "HDF Users Discussion List" <hdf-forum@lists.hdfgroup.org<mailto:hdf-forum@lists.hdfgroup.org>> 抄送: "HDF Helpdesk" <h...@hdfgroup.org<mailto:h...@hdfgroup.org>> 主题: Re: [Hdf-forum] Errors when install HDF5 Hello Jie, It looks like your HDF5 library is good. (Though the prefix directory specified on the configure line is “usr/local/hdf5” and *not* “/usr/local/hdf5”.) Regarding the error, there are examples in the share/ directory of the built binaries that the “make check-install” is unsuccessfully attempting to compile and run. It is possible that the “make check-install” cannot find the HDF5 libraries. You could try setting the path to the HDF5 libraries in LD_LIBRARY_PATH to see if that helps (if building shared libraries). You can also run the examples manually to see if that yields more information: • Go to the location of your built HDF5 binaries. You will see a “share” directory (in addition to include/, lib/, etc..). • Go into share/hdf5_examples/ and run “run-all-ex.sh”. Do the examples run properly? -Barbara ======================================================== Barbara Jones, The HDF Group Helpdesk, h...@hdfgroup.org<mailto:h...@hdfgroup.org> Support Services: https://www.hdfgroup.org/support/ ======================================================== From: Hdf-forum [mailto:hdf-forum-boun...@lists.hdfgroup.org<mailto:hdf-forum-boun...@lists.hdfgroup.org>] On Behalf Of ?? Sent: Monday, November 20, 2017 3:24 AM To: hdf-forum@lists.hdfgroup.org<mailto:hdf-forum@lists.hdfgroup.org> Subject: [Hdf-forum] Errors when install HDF5 Hi all: Recently I am going to use HDF5, I install it with following command: “ ./configure —prefix=usr/local/hdf5 —enable-fortran make make check make install make check-install " Everything goes well but when I run “make check-install”, it has some errors say: “ Testing run-fortran-ex.sh ===================== ################# h5_crtdat ################# Assembler messages: error: can't create h5_crtdat.o: for write messed up compiling h5_crtdat.f90 rm: cannot remove `*.o': No such file or directory rm: cannot remove `*.h5': No such file or directory Makefile:1207: recipe for target ‘installcheck-local’ failed make[3]: *** [installcheck-local] Error 1 make[3]: Leaving directory `/home/ustc/Download/hdf5-1.10.1/fortran/examples’ Makefile:1244: recipe for target ’installcheck-local’ failed make[2]: *** [installcheck-local] Error 1 make[2]: Leaving directory `/home/ustc/Download/hdf5-1.10.1/fortran’ Makefile:811: recipe for target ‘installcheck-recursive’ failed make[1]: *** [installcheck-recursive] Error 1 make[1]: Leaving directory `/home/ustc/Download/hdf5-1.10.1/fortran’ Makefile:650: recipe for target ‘installcheck-recursive’ failed make: *** [installcheck-recursive] Error 1 “ I have google a lot but it seems like a bug that haven’t been solved. I am soooo puzzled by this problem, please help me. My Ubuntu version is 16.04, ifort version is 18.0.1. Best, Jie _______________________________________________ Hdf-forum is for HDF software users discussion. Hdf-forum@lists.hdfgroup.org<mailto:Hdf-forum@lists.hdfgroup.org> http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org Twitter: https://twitter.com/hdf5 <check.out><config.log><configure.out><make.out>
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