unable to 'make' slurm

[saikrishnarallabandi]

I am following the tutorial for 16.04 and hit a road block after the configure step.

Here is a brief trace:

sh5util.o: In function _extract_series_table': /storage/slurm-17.11.12/src/plugins/acct_gather_profile/hdf5/sh5util/sh5util.c:1080: undefined reference to H5PTopen'
sh5util.o: In function _extract_totals': /storage/slurm-17.11.12/src/plugins/acct_gather_profile/hdf5/sh5util/sh5util.c:936: undefined reference to H5PTget_num_packets'
/storage/slurm-17.11.12/src/plugins/acct_gather_profile/hdf5/sh5util/sh5util.c:940: undefined reference to H5PTget_next' sh5util.o: In function _extract_series_table':
/storage/slurm-17.11.12/src/plugins/acct_gather_profile/hdf5/sh5util/sh5util.c:1090: undefined reference to H5PTget_num_packets' /storage/slurm-17.11.12/src/plugins/acct_gather_profile/hdf5/sh5util/sh5util.c:1095: undefined reference to H5PTget_next'
/storage/slurm-17.11.12/src/plugins/acct_gather_profile/hdf5/sh5util/sh5util.c:1117: undefined reference to H5PTclose' /storage/slurm-17.11.12/src/plugins/acct_gather_profile/hdf5/sh5util/sh5util.c:1126: undefined reference to H5PTclose'
/storage/slurm-17.11.12/src/plugins/acct_gather_profile/hdf5/sh5util/sh5util.c:1127: undefined reference to H5PTclose' sh5util.o: In function _extract_item_step':
/storage/slurm-17.11.12/src/plugins/acct_gather_profile/hdf5/sh5util/sh5util.c:1552: undefined reference to H5PTopen' /storage/slurm-17.11.12/src/plugins/acct_gather_profile/hdf5/sh5util/sh5util.c:1556: undefined reference to H5PTget_num_packets'
sh5util.o: In function _item_analysis_uint': /storage/slurm-17.11.12/src/plugins/acct_gather_profile/hdf5/sh5util/sh5util.c:1276: undefined reference to H5PTget_next'
sh5util.o: In function _item_analysis_double': /storage/slurm-17.11.12/src/plugins/acct_gather_profile/hdf5/sh5util/sh5util.c:1377: undefined reference to H5PTget_next'
sh5util.o: In function _extract_item_step': /storage/slurm-17.11.12/src/plugins/acct_gather_profile/hdf5/sh5util/sh5util.c:1591: undefined reference to H5PTclose'
/storage/slurm-17.11.12/src/plugins/acct_gather_profile/hdf5/sh5util/sh5util.c:1606: undefined reference to `H5PTclose'
collect2: error: ld returned 1 exit status
Makefile:590: recipe for target 'sh5util' failed
make[6]: *** [sh5util] Error 1
make[6]: Leaving directory '/storage/slurm-17.11.12/src/plugins/acct_gather_profile/hdf5/sh5util'
Makefile:734: recipe for target 'all-recursive' failed
make[5]: *** [all-recursive] Error 1
make[5]: Leaving directory '/storage/slurm-17.11.12/src/plugins/acct_gather_profile/hdf5'
Makefile:540: recipe for target 'all-recursive' failed
make[4]: *** [all-recursive] Error 1
make[4]: Leaving directory '/storage/slurm-17.11.12/src/plugins/acct_gather_profile'
Makefile:569: recipe for target 'all-recursive' failed
make[3]: *** [all-recursive] Error 1
make[3]: Leaving directory '/storage/slurm-17.11.12/src/plugins'
Makefile:569: recipe for target 'all-recursive' failed
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory '/storage/slurm-17.11.12/src'
Makefile:696: recipe for target 'all-recursive' failed
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory '/storage/slurm-17.11.12'
Makefile:595: recipe for target 'all' failed
make: *** [all] Error 2

I am also attaching the full trace for reference.
log_make.txt

[mknoxnv]

Looks like you need to install hdf5 library and Dev packages. Please let me know if that fixes the problem.

[saikrishnarallabandi]

Thanks for the response. i do have hdf5. What is the dev package you are referring to?

[mknoxnv]

Do you have libhdf5-dev installed?

[saikrishnarallabandi]

yes

[saikrishnarallabandi]

sudo apt-get install libhdf5-dev
Reading package lists... Done
Building dependency tree
Reading state information... Done
libhdf5-dev is already the newest version (1.8.16+docs-4ubuntu1.1).
The following packages were automatically installed and are no longer required:
linux-headers-4.15.0-47 linux-headers-4.15.0-47-generic linux-headers-4.15.0-50 linux-headers-4.15.0-50-generic linux-image-4.15.0-47-generic linux-image-4.15.0-50-generic linux-modules-4.15.0-47-generic linux-modules-4.15.0-50-generic
linux-modules-extra-4.15.0-47-generic linux-modules-extra-4.15.0-50-generic
Use 'sudo apt autoremove' to remove them.
0 upgraded, 0 newly installed, 0 to remove and 85 not upgraded.

[mknoxnv]

Hmm, do you need hdf5 support? If not you could try rerunning the configure with --with-hdf5=no.

[saikrishnarallabandi]

sweet. thanks. have another issue down the line. will close this one

[saikrishnarallabandi]

Here:

#3 (comment)

[cowarder]

Hi, @saikrishnarallabandi I met the same problem as you, how did you solve this?

[realWilliamChin]

Hi, @cowarder I met the same problem as you, how did you solve this?

[CCSun21]

Hi, @realWilliamChin ,I met the same problem as you, but I found my base anaconda enviroment was activated, the problem was solved after I decativated it.

[yanchenmochen]

Looks like you need to install hdf5 library and Dev packages. Please let me know if that fixes the problem.

I have tried this method, but cannot resolve this problem, I donnot know why

[yanchenmochen]

Hi, @realWilliamChin ,I met the same problem as you, but I found my base anaconda enviroment was activated, the problem was solved after I decativated it.

I handle it also, conda deactivate, then I can build the rpm

[yanchenmochen]

@realWilliamChin It is the way I resolve problem. Thank you very much

[amulil]

Hi, @saikrishnarallabandi I met the same problem as you, how did you solve this?

[spkane]

For Ubuntu 20.04 I ended up adding --with-hdf5=no to ./configure to work around the issue, since at the moment, I don't have any specific need for this functionality.