[slurm-users] slurm-19.05 link error

[Weiguang Chen]

Hi,



I’m installing slurm in my Archlinux Server.

At the beginning, I used AUR helper yaourt to install it.

yaourt -S slurm-llnl

But an error occur while compiling sh5util, as follow:

libtool: link: gcc -DNUMA_VERSION1_COMPATIBILITY -march=x86-64
-mtune=generic -O2 -pipe -pthread -ggdb3 -Wall -g -O1 -fno-strict-aliasing
-Wl,-O1 -Wl,--sort-common -Wl,--as-needed -Wl

,-z -Wl,relro -Wl,-z -Wl,lazy -o .libs/sh5util sh5util.o
-Wl,-rpath=/usr/lib/slurm -Wl,--export-dynamic  -L/home/zznu/miniconda3/lib
-L../../../../../src/api/.libs
/tmp/yaourt-tmp-zznu/aur-slurm-llnl/src/slurm-slurm-19-05-0-1/src/api/.libs/libslurmfull.so
../.libs/libhdf5_api.a -lm -ldl -lz -lpthread -lrt -lhdf5 -pthread
-Wl,-rpath -Wl,/usr/lib/slurm

/usr/bin/ld: sh5util.o: in function
`_extract_series_table':
/tmp/yaourt-tmp-zznu/aur-slurm-llnl/src/slurm-slurm-19-05-0-1/src/plugins/acct_gather_profile/hdf5/sh5util/sh5util.c:1079:
undefined reference to `H5PTopen'

/usr/bin/ld: sh5util.o: in function
`_extract_totals':

/tmp/yaourt-tmp-zznu/aur-slurm-llnl/src/slurm-slurm-19-05-0-1/src/plugins/acct_gather_profile/hdf5/sh5util/sh5util.c:935:
undefined reference to `H5PTget_num_packets'

/usr/bin/ld:
/tmp/yaourt-tmp-zznu/aur-slurm-llnl/src/slurm-slurm-19-05-0-1/src/plugins/acct_gather_profile/hdf5/sh5util/sh5util.c:939:
undefined reference to `H5PTget_next'

/usr/bin/ld: sh5util.o: in function `_extract_series_table':

/tmp/yaourt-tmp-zznu/aur-slurm-llnl/src/slurm-slurm-19-05-0-1/src/plugins/acct_gather_profile/hdf5/sh5util/sh5util.c:1089:
undefined reference to `H5PTget_num_packets'

/usr/bin/ld:
/tmp/yaourt-tmp-zznu/aur-slurm-llnl/src/slurm-slurm-19-05-0-1/src/plugins/acct_gather_profile/hdf5/sh5util/sh5util.c:1094:
undefined reference to `H5PTget_next'

/usr/bin/ld:
/tmp/yaourt-tmp-zznu/aur-slurm-llnl/src/slurm-slurm-19-05-0-1/src/plugins/acct_gather_profile/hdf5/sh5util/sh5util.c:1125:
undefined reference to `H5PTclose'

/usr/bin/ld:
/tmp/yaourt-tmp-zznu/aur-slurm-llnl/src/slurm-slurm-19-05-0-1/src/plugins/acct_gather_profile/hdf5/sh5util/sh5util.c:1126:
undefined reference to `H5PTclose'

/usr/bin/ld:
/tmp/yaourt-tmp-zznu/aur-slurm-llnl/src/slurm-slurm-19-05-0-1/src/plugins/acct_gather_profile/hdf5/sh5util/sh5util.c:1116:
undefined reference to `H5PTclose'

/usr/bin/ld: sh5util.o: in function `_extract_item_step':

/tmp/yaourt-tmp-zznu/aur-slurm-llnl/src/slurm-slurm-19-05-0-1/src/plugins/acct_gather_profile/hdf5/sh5util/sh5util.c:1551:
undefined reference to `H5PTopen'

/usr/bin/ld:
/tmp/yaourt-tmp-zznu/aur-slurm-llnl/src/slurm-slurm-19-05-0-1/src/plugins/acct_gather_profile/hdf5/sh5util/sh5util.c:1555:
undefined reference to `H5PTget_num_packets'   /usr/bin/ld: sh5util.o: in
function
`_item_analysis_uint':
/tmp/yaourt-tmp-zznu/aur-slurm-llnl/src/slurm-slurm-19-05-0-1/src/plugins/acct_gather_profile/hdf5/sh5util/sh5util.c:1275:
undefined reference to `H5PTget_next'                       /usr/bin/ld:
sh5util.o: in function
`_extract_item_step':


/tmp/yaourt-tmp-zznu/aur-slurm-llnl/src/slurm-slurm-19-05-0-1/src/plugins/acct_gather_profile/hdf5/sh5util/sh5util.c:1590:
undefined reference to `H5PTclose'                          /usr/bin/ld:
sh5util.o: in function
`_item_analysis_double':
/tmp/yaourt-tmp-zznu/aur-slurm-llnl/src/slurm-slurm-19-05-0-1/src/plugins/acct_gather_profile/hdf5/sh5util/sh5util.c:1376:
undefined reference to `H5PTget_next'

/usr/bin/ld: sh5util.o: in function `_extract_item_step':

/tmp/yaourt-tmp-zznu/aur-slurm-llnl/src/slurm-slurm-19-05-0-1/src/plugins/acct_gather_profile/hdf5/sh5util/sh5util.c:1605:
undefined reference to `H5PTclose'                          collect2:
error: ld returned 1 exit
status


make[6]: *** [Makefile:572: sh5util] Error
1
make[6]: Leaving directory
'/tmp/yaourt-tmp-zznu/aur-slurm-llnl/src/slurm-slurm-19-05-0-1/src/plugins/acct_gather_profile/hdf5/sh5util'
make[5]: *** [Makefile:722: all-recursive] Error
1
                                                           make[5]: Leaving
directory
'/tmp/yaourt-tmp-zznu/aur-slurm-llnl/src/slurm-slurm-19-05-0-1/src/plugins/acct_gather_profile/hdf5'
make[4]: *** [Makefile:521: all-recursive] Error
1
make[4]: Leaving directory
'/tmp/yaourt-tmp-zznu/aur-slurm-llnl/src/slurm-slurm-19-05-0-1/src/plugins/acct_gather_profile'
make[3]: *** [Makefile:552: all-recursive] Error
1
                       make[3]: Leaving directory
'/tmp/yaourt-tmp-zznu/aur-slurm-llnl/src/slurm-slurm-19-05-0-1/src/plugins'
make[2]: *** [Makefile:546: all-recursive] Error
1
make[2]: Leaving directory
'/tmp/yaourt-tmp-zznu/aur-slurm-llnl/src/slurm-slurm-19-05-0-1/src'
                                                            make[1]: ***
[Makefile:674: all-recursive] Error
1
make[1]: Leaving directory
'/tmp/yaourt-tmp-zznu/aur-slurm-llnl/src/slurm-slurm-19-05-0-1'



Then, I directly download the source code from slurm official website,
./configure & make. Same error occored.

I don’t know what the problem is, how to fix it.

Thanks.

-- 
*****************************************************************************
*        Chen, Weiguang, Ph.D
*   Quantum Materials Research Center &
*   College of Physics and Electronic Engineering
*   No.6, Yingcai Road, Physics Building  Rm#3511
*   Zhengzhou Normal University, Zhengzhou, 450044 Henan, China
*
*   Tel: 86-13783677861; Fax: 86-371-65502273;
*   Email: chenweiguang82 at gmail.com; chenweiguang82 at 126.com
****************************************************************************
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