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Bug 625794 - sci-libs/silo-4.10.2 will not build with USE hdf5: ../../src/.libs/libsiloh5.so: undefined reference to `H5Pset_fapl_mpiposix'
Summary: sci-libs/silo-4.10.2 will not build with USE hdf5: ../../src/.libs/libsiloh5....
Status: RESOLVED OBSOLETE
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: Current packages (show other bugs)
Hardware: AMD64 Linux
: Normal normal
Assignee: Gentoo Cluster Team
URL:
Whiteboard:
Keywords:
Depends on:
Blocks:
 
Reported: 2017-07-21 01:48 UTC by deference
Modified: 2022-01-19 22:01 UTC (History)
4 users (show)

See Also:
Package list:
Runtime testing required: ---

Attachments
build.log (build-silo.txt,288.49 KB, text/plain)
2017-07-21 01:48 UTC, deference 		Details
emerge --info (emergeinfo-silo.txt,31.77 KB, text/plain)
2017-07-21 01:48 UTC, deference 		Details
View All Add an attachment (proposed patch, testcase, etc.)

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Description deference 2017-07-21 01:48:18 UTC 
libtool: link: x86_64-pc-linux-gnu-g++ -pipe -O2 -Wl,-O1 -Wl,--as-needed -o .libs/silock silock.o  -L/usr/lib ../../src/.libs/libsiloh5.so -L/usr/lib64 /usr/lib64/libhdf5.so /usr/lib64/libsz.so -ldl -lz -lm
../../src/.libs/libsiloh5.so: undefined reference to `H5Pset_fapl_mpiposix'
collect2: error: ld returned 1 exit status

[ebuild   R   ] sci-libs/silo-4.10.2  USE="hdf5* qt4 silex static-libs {-test}"
Comment 1 deference 2017-07-21 01:48:36 UTC 
Created attachment 486190 [details]
build.log
Comment 2 deference 2017-07-21 01:48:45 UTC 
Created attachment 486192 [details]
emerge --info
Comment 3 Sławek Lis (RETIRED) gentoo-dev 2017-07-24 06:06:01 UTC 
Which version of sci-libs/hdf5 you have installed?
Comment 4 deference 2017-07-28 00:13:30 UTC 
I don't know if I upgraded between the bug reports creation and currently.
I currently have version 1.8.18 installed.
Comment 5 Sławek Lis (RETIRED) gentoo-dev 2017-07-28 07:04:50 UTC 
This is caused by sci-libs/hdf5 built with mpi use flag.
Silo uses old function name, which is deprecated and removed since hdf5-1.8.13.
https://support.hdfgroup.org/HDF5/doc/RM/RM_H5P.html#Property-SetFaplMpiPosix

I've attached a patch, please verify. It builds fine for me, but I'm not sure about further working.
Comment 6 Ionen Wolkens gentoo-dev 2022-01-19 22:01:07 UTC 
I unmasked mpi on hdf5 and gave this a try, builds fine as far as I can tell.

Likely got fixed by something in the last few years, but haven't looked deeper.