Errors when install HDF5

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Errors when install HDF5

jiejiang
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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Re: Errors when install HDF5

bljones

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, [hidden email]

Support Services:  https://www.hdfgroup.org/support/

========================================================

 

 

 

From: Hdf-forum [mailto:[hidden email]] On Behalf Of ??
Sent: Monday, November 20, 2017 3:24 AM
To: [hidden email]
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.
[hidden email]
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: https://twitter.com/hdf5
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Re: Errors when install HDF5

jiejiang
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" <[hidden email]>
发送时间:2017-11-20 23:36:39 (星期一)
收件人: "HDF Users Discussion List" <[hidden email]>
抄送: "HDF Helpdesk" <[hidden email]>
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, [hidden email]

Support Services:  https://www.hdfgroup.org/support/

========================================================

 

 

 

From: Hdf-forum [mailto:[hidden email]] On Behalf Of ??
Sent: Monday, November 20, 2017 3:24 AM
To: [hidden email]
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.
[hidden email]
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: https://twitter.com/hdf5
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Re: Errors when install HDF5

Scot Breitenfeld
Did you patch the Fortran source for Intel 18? 


Scot

On Nov 30, 2017, at 8:13 AM, 江捷 <[hidden email]> 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" <[hidden email]>
发送时间:2017-11-20 23:36:39 (星期一)
收件人: "HDF Users Discussion List" <[hidden email]>
抄送: "HDF Helpdesk" <[hidden email]>
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, [hidden email]
========================================================
 
 
From: Hdf-forum [mailto:[hidden email]] On Behalf Of ??
Sent: Monday, November 20, 2017 3:24 AM
To: [hidden email]
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.
[hidden email]
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: https://twitter.com/hdf5


_______________________________________________
Hdf-forum is for HDF software users discussion.
[hidden email]
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: https://twitter.com/hdf5
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Re: [SPAM] Re: Errors when install HDF5

jiejiang
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" <[hidden email]>
发送时间:2017-11-30 23:09:16 (星期四)
收件人: "HDF Users Discussion List" <[hidden email]>
抄送:
主题: [SPAM] Re: [Hdf-forum] Errors when install HDF5

Did you patch the Fortran source for Intel 18? 


Scot

On Nov 30, 2017, at 8:13 AM, 江捷 <[hidden email]> 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" <[hidden email]>
发送时间:2017-11-20 23:36:39 (星期一)
收件人: "HDF Users Discussion List" <[hidden email]>
抄送: "HDF Helpdesk" <[hidden email]>
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, [hidden email]
========================================================
 
 
From: Hdf-forum [mailto:[hidden email]] On Behalf Of ??
Sent: Monday, November 20, 2017 3:24 AM
To: [hidden email]
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.
[hidden email]
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: https://twitter.com/hdf5


_______________________________________________
Hdf-forum is for HDF software users discussion.
[hidden email]
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: https://twitter.com/hdf5

check.out (1M) Download Attachment
config.log (2M) Download Attachment
configure.out (38K) Download Attachment
make.out (877K) Download Attachment
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Re: [SPAM] Errors when install HDF5

Scot Breitenfeld
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 <[hidden email]> 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" <[hidden email]>
发送时间:2017-11-30 23:09:16 (星期四)
收件人: "HDF Users Discussion List" <[hidden email]>
抄送:
主题: [SPAM] Re: [Hdf-forum] Errors when install HDF5

Did you patch the Fortran source for Intel 18? 


Scot

On Nov 30, 2017, at 8:13 AM, 江捷 <[hidden email]> 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" <[hidden email]>
发送时间:2017-11-20 23:36:39 (星期一)
收件人: "HDF Users Discussion List" <[hidden email]>
抄送: "HDF Helpdesk" <[hidden email]>
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, [hidden email]
========================================================
 
 
From: Hdf-forum [mailto:[hidden email]] On Behalf Of ??
Sent: Monday, November 20, 2017 3:24 AM
To: [hidden email]
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.
[hidden email]
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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Re: [SPAM] Errors when install HDF5

jiejiang
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 <[hidden email]> 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 <[hidden email]> 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" <[hidden email]>
发送时间:2017-11-30 23:09:16 (星期四)
收件人: "HDF Users Discussion List" <[hidden email]>
抄送:
主题: [SPAM] Re: [Hdf-forum] Errors when install HDF5

Did you patch the Fortran source for Intel 18? 


Scot

On Nov 30, 2017, at 8:13 AM, 江捷 <[hidden email]> 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" <[hidden email]>
发送时间:2017-11-20 23:36:39 (星期一)
收件人: "HDF Users Discussion List" <[hidden email]>
抄送: "HDF Helpdesk" <[hidden email]>
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, [hidden email]
========================================================
 
 
From: Hdf-forum [mailto:[hidden email]] On Behalf Of ??
Sent: Monday, November 20, 2017 3:24 AM
To: [hidden email]
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.
[hidden email]
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: https://twitter.com/hdf5

<check.out><config.log><configure.out><make.out>



_______________________________________________
Hdf-forum is for HDF software users discussion.
[hidden email]
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: https://twitter.com/hdf5
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Re: [SPAM] Errors when install HDF5

bljones

Hi Jie,

 

We can reproduce this issue here and will plan to fix it for the HDF5-1.10.2 release (Spring 2018).

 

-Barbara

[hidden email]

 

From: Hdf-forum [mailto:[hidden email]] 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



2017121日,下午11:53Scot Breitenfeld <[hidden email]> 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 <[hidden email]> 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//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//hdf5-1.10.1/testpar'

Makefile:1380: recipe for target 'test' failed

make[2]: *** [test] Error 2

make[2]: Leaving directory '/home/ustc//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//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" <[hidden email]>
发送时间:2017-11-30 23:09:16 (星期四)
收件人: "HDF Users Discussion List" <[hidden email]>
抄送:
: [SPAM] Re: [Hdf-forum] Errors when install HDF5

Did you patch the Fortran source for Intel 18? 

 

 

Scot

 

On Nov 30, 2017, at 8:13 AM, 江捷 <[hidden email]> 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" <[hidden email]>
发送时间:2017-11-20 23:36:39 (星期一)
收件人: "HDF Users Discussion List" <[hidden email]>
抄送: "HDF Helpdesk" <[hidden email]>
: 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, [hidden email]

Support Services:  https://www.hdfgroup.org/support/

========================================================

 

 

 

From: Hdf-forum [mailto:[hidden email]] On Behalf Of ??
Sent: Monday, November 20, 2017 3:24 AM
To: [hidden email]
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.
[hidden email]
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: https://twitter.com/hdf5

 

<check.out><config.log><configure.out><make.out>

 

 


_______________________________________________
Hdf-forum is for HDF software users discussion.
[hidden email]
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
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Re: Errors when install HDF5

jiejiang
Hello,

I have use another computer running CentOS release 6.6 (Final), ifort 2016, version 16.0.4.258 to install HDF5-1.10.1, my command is following:

"FC=/exports/intel/impi/5.1.3.258/intel64/bin/mpif90 ./configure --enable-parallel --prefix=/exports/hdf5-1.10.1 --enable-fortran --enable-shared 
make"
Everything is fine but when I run “make check”, it has the following errors:
“make[4]: *** [testphdf5.chkexe_] Error 1
make[4]: Leaving directory `/home/Kong/software/hdf5-1.10.1/testpar'
make[3]: *** [build-check-p] Error 1
make[3]: Leaving directory `/home/Kong/software/hdf5-1.10.1/testpar'
make[2]: *** [test] Error 2
make[2]: Leaving directory `/home/Kong/software/hdf5-1.10.1/testpar'
make[1]: *** [check-am] Error 2
make[1]: Leaving directory `/home/Kong/software/hdf5-1.10.1/testpar'
make: *** [check-recursive] Error 1"

I have attached the configure.out, make.out, check.out and config.log, please help me to fix this problem. Thank you very much.

Best Regards
Jie Jiang






在 2017年12月7日,上午2:41,Barbara Jones <[hidden email]> 写道:

Hi Jie,
 
We can reproduce this issue here and will plan to fix it for the HDF5-1.10.2 release (Spring 2018).
 
-Barbara
From: Hdf-forum [[hidden email]] 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


 2017121日,下午11:53Scot Breitenfeld <[hidden email]> 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 <[hidden email]> 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//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//hdf5-1.10.1/testpar'
Makefile:1380: recipe for target 'test' failed
make[2]: *** [test] Error 2
make[2]: Leaving directory '/home/ustc//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//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" <[hidden email]>
发送时间:2017-11-30 23:09:16 (星期四)
收件人: "HDF Users Discussion List" <[hidden email]>
抄送: 
: [SPAM] Re: [Hdf-forum] Errors when install HDF5

Did you patch the Fortran source for Intel 18?  
 
 
Scot
 
On Nov 30, 2017, at 8:13 AM, 江捷 <[hidden email]> 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" <[hidden email]>
发送时间:2017-11-20 23:36:39 (星期一)
收件人: "HDF Users Discussion List" <[hidden email]>
抄送: "HDF Helpdesk" <[hidden email]>
: 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, [hidden email]
========================================================
 
 
 
From: Hdf-forum [mailto:[hidden email]] On Behalf Of ??
Sent: Monday, November 20, 2017 3:24 AM
To: [hidden email]
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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Hdf-forum is for HDF software users discussion.
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Twitter: https://twitter.com/hdf5
 
<check.out><config.log><configure.out><make.out>
 
 
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Hdf-forum is for HDF software users discussion.
[hidden email]
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Twitter: https://twitter.com/hdf5


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Hdf-forum is for HDF software users discussion.
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Re: Errors when install HDF5

jiejiang
Hello, Barbara,

Thank you sooooo much for your reply, I am sorry to reply you late. I have installed by running “yum install hdf5 hdf5-devel”. Although I don’t know which version I have installed, and the program I need runs well. I just focus the program so I ignore the error I have meet. By the way, thank you for your concern.

Have a nice day.
Jie Jiang

在 2017年12月7日,下午12:06,江捷 <[hidden email]> 写道:

<config.log>


_______________________________________________
Hdf-forum is for HDF software users discussion.
[hidden email]
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: https://twitter.com/hdf5