We can reproduce this issue here and will plan to fix it for the HDF5-1.10.2 release (Spring 2018).
···
From: Hdf-forum [mailto:hdf-forum-bounces@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 <brtnfld@hdfgroup.org<mailto:brtnfld@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 <jiejiang@mail.ustc.edu.cn<mailto:jiejiang@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" <brtnfld@hdfgroup.org<mailto:brtnfld@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 <jiejiang@mail.ustc.edu.cn<mailto:jiejiang@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" <bljones@hdfgroup.org<mailto:bljones@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" <help@hdfgroup.org<mailto:help@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
From: Hdf-forum [mailto:hdf-forum-bounces@lists.hdfgroup.org<mailto:hdf-forum-bounces@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
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<check.out><config.log><configure.out><make.out>
