H5repack error - make check


#1

Hi,

I am trying to install HDF5 on a Ubuntu 16.04 with the following commands:

$ ./configure --prefix=/usr/local/hdf5 --enable-build-mode=production
$ make
$ make check

However, after the latter I get the following errors:

h5repack tests failed with 1 errors.
Command exited with non-zero status 1
3.20user 1.01system 0:03.73elapsed 112%CPU (0avgtext+0avgdata 13256maxresident)k
0inputs+20624outputs (0major+602220minor)pagefaults 0swaps
Makefile:1449: recipe for target ‘h5repack.sh.chkexe_’ failed
make[6]: *** [h5repack.sh.chkexe_] Error 1
make[6]: Leaving directory ‘/home/leonardo/Downloads/hdf5-1.10.1/tools/test/h5repack’
Makefile:1397: recipe for target ‘build-check-s’ failed
make[5]: *** [build-check-s] Error 2
make[5]: Leaving directory ‘/home/leonardo/Downloads/hdf5-1.10.1/tools/test/h5repack’
Makefile:1392: recipe for target ‘test’ failed
make[4]: *** [test] Error 2
make[4]: Leaving directory ‘/home/leonardo/Downloads/hdf5-1.10.1/tools/test/h5repack’
Makefile:1178: recipe for target ‘check-am’ failed
make[3]: *** [check-am] Error 2
make[3]: Leaving directory ‘/home/leonardo/Downloads/hdf5-1.10.1/tools/test/h5repack’
Makefile:807: recipe for target ‘check-recursive’ failed
make[2]: *** [check-recursive] Error 1
make[2]: Leaving directory ‘/home/leonardo/Downloads/hdf5-1.10.1/tools/test’
Makefile:805: recipe for target ‘check-recursive’ failed
make[1]: *** [check-recursive] Error 1
make[1]: Leaving directory ‘/home/leonardo/Downloads/hdf5-1.10.1/tools’
Makefile:650: recipe for target ‘check-recursive’ failed
make: *** [check-recursive] Error 1

I would appreciate any help on this.


#2

greetings!

LinuxMint 18 here with ubuntu 16.04 under her skirt. Luckily last night all I did was compiling the same exact version of HDF5 (testing h5cpp object mapper) so I still have the set up.

I didn’t specify production – as it is the default, and now running make check for you:

(some time later)

checked out fine… no error here.

best,

steven

LSB Version: core-9.20160110ubuntu0.2-amd64:core-9.20160110ubuntu0.2-noarch:security-9.20160110ubuntu0.2-amd64:security-9.20160110ubuntu0.2-noarch

Distributor ID: LinuxMint

Description: Linux Mint 18 Sarah

Release: 18

Codename: sara


#3

I tried doing a make clean and then doing everything again but I still get the same error.

Can you tell me if you included any other flags other than the ones I used?


#4

can you please follow these instructions and see if the error still persist?

git clone https://github.com/live-clones/hdf5.git

cd hdf5 && git checkout hdf5-1_10_1 && ./configure --prefix=/usr/local && make && sudo make check

please note the git ‘tag’ and that no ‘production’ is specified; because it is the default settings.

steve


#5

On the command line you suggested, I get the error “not a git repository”.

I keep getting the same error. I even tried doing it with the 1.8.20 version but the error remains:

h5repack tests failed with 1 errors.
Command exited with non-zero status 1
3.00user 1.10system 0:03.17elapsed 129%CPU (0avgtext+0avgdata 12452maxresident)k
0inputs+18208outputs (0major+553728minor)pagefaults 0swaps
Makefile:1461: recipe for target ‘h5repack.sh.chkexe_’ failed
make[5]: *** [h5repack.sh.chkexe_] Error 1
make[5]: Leaving directory ‘/home/leonardo/Downloads/hdf5-1.8.20/tools/h5repack’
Makefile:1409: recipe for target ‘build-check-s’ failed
make[4]: *** [build-check-s] Error 2
make[4]: Leaving directory ‘/home/leonardo/Downloads/hdf5-1.8.20/tools/h5repack’
Makefile:1404: recipe for target ‘test’ failed
make[3]: *** [test] Error 2
make[3]: Leaving directory ‘/home/leonardo/Downloads/hdf5-1.8.20/tools/h5repack’
Makefile:1187: recipe for target ‘check-am’ failed
make[2]: *** [check-am] Error 2
make[2]: Leaving directory ‘/home/leonardo/Downloads/hdf5-1.8.20/tools/h5repack’
Makefile:743: recipe for target ‘check-recursive’ failed
make[1]: *** [check-recursive] Error 1
make[1]: Leaving directory ‘/home/leonardo/Downloads/hdf5-1.8.20/tools’
Makefile:586: recipe for target ‘check-recursive’ failed
make: *** [check-recursive] Error 1

Is there anything I should install/configure prior to the installation?


#6

here is the list of tools:

gcc (Ubuntu 5.4.0-6ubuntu1~16.04.9) 5.4.0 20160609

automake (GNU automake) 1.15

GNU Make 4.1

steve


#7

Hi there again. Seem like my tools are pretty much the same as yours

gcc (Ubuntu 5.4.0-6ubuntu1~16.04.9) 5.4.0 20160609

GNU Make 4.1
Built for x86_64-pc-linux-gnu

automake (GNU automake) 1.15

but I still didn’t manage to get it working. I have tracked down an extra line where the error occurs that might be useful:

Testing h5repack -f GZIP=1 PASSED
Verifying h5diff output h5repack_objs.h5 out-gt_mallocsize.h5repack_obFAILED
committed_dt h5repack_named_dtypes.h5
Testing h5repack PASSED

Does this add any information? I feel like there is something I’m not doing and that’s why I’m getting the error.


#8

Hi leow,
I see this post was a long time ago, but I just run into a very similar error with hdf5-1.10.5.
I would like to ask, did you manage to solve this problem? :slight_smile:
Thanks!


#9

Hi there,

I did manage to get it working, but I’m not exactly sure if what I will tell you will be enough. You might need another flag (more below).

The issue I was having was that some of the tests were failing, but according to a few posts a found (which I have no idea where anymore), some of those would fail. So when running $: sudo make check, I did $: sudo make -i check to ignore the errors and proceed anyway. With that flag everything worked, if I remember correctly.

Sorry for not being clear, it was quite a while back :~

Cheers.