Package Details: scotch 6.0.4-3

Git Clone URL: https://aur.archlinux.org/scotch.git (read-only)
Package Base: scotch
Description: Software package and libraries for graph, mesh and hypergraph partitioning, static mapping, and sparse matrix block ordering. This is the all-inclusive version (MPI/serial/esmumps).
Upstream URL: http://www.labri.fr/perso/pelegrin/scotch/
Licenses: custom:CeCILL-C
Conflicts: ptscotch-openmpi, scotch_esmumps, scotch_esmumps5
Provides: ptscotch, ptscotch-openmpi, scotch_esmumps, scotch_ptesmumps
Submitter: None
Maintainer: ioquatix
Last Packager: ioquatix
Votes: 30
Popularity: 0.002638
First Submitted: 2006-11-07 17:51
Last Updated: 2017-01-25 00:12

Latest Comments

ioquatix commented on 2018-02-26 01:53

I am communicating with the original developer and I hope there would be a good solution soon.

phleva commented on 2018-02-23 21:21

Just want to thank @AsmundEr and @sigvald and maybe help others along the way. Trying to build on a virtual machine with only one processor I ran into the mpirun limitation forementioned. Adding the --oversubscribe flag in the pkgbuild got rid of the error. Also, managed to clear the other errors by cleaning before and having the package localy. "pacman -sric --cleanbuild"

ioquatix commented on 2018-02-19 22:25

@sigvald I have passed your feedback upstream and will attempt to address your issues when I hear back.

sigvald commented on 2018-02-19 15:18

So I managed to install it and the mpirun problem was indeed a problem on my computer and not on the package per se. I'll give workarounds for both issues:

So for the SSL problem I don't know what's up with the SSL of that site. For those who are ready to take the chances of trusting this site, download the source file (http://gforge.inria.fr/frs/download.php/file/34618/scotch_6.0.4.tar.gz) into your scotch folder and run "makepkg -sri". Since the file is already there, it won't complain that the certificate of the site is not trusted.

Second, the testing of scotch involved running something on 4 processes while my laptop only have 2 cores. This was not a problem with my old installation of OpenMPI (perhaps an OpenMPI 3 thing?). If you can't run "mpirun -n 4 echo hello" then you have this problem too. However, adding "--oversubscribe" allows you to run 4 processes. I made makepkg add this flag to the test by adding a sed-line in the the check() function in the PKGBUILD file as follows:

check() {
  cd "${srcdir}/${pkgname}_${pkgver}/src"

  sed -i 's/mpirun/mpirun --oversubscribe/' check/Makefile

  make check LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:../../lib"
  make ptcheck LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:../../lib"
}

And that made it work. May I suggest adding that sed-line permanently to this PKGBUILD?

sigvald commented on 2018-02-19 12:46

It seems that this error is because the source of the .tar.gz file used to be on an http:// adress but now it is forwarded to an https:// adress (but otherwise the same adress) and my system cannot verify the validity of the certificate. Of course, neither can I, but if you decide to "trust" the source anyway, you can download the .tar.gz-file to your clone of the scotch folder and run makepkg -sri again. Since the source file is already there it won't use curl to try to download it. That gets us one step further, but now I get this one:

mpirun -n 4 ./test_scotch_dgraph_check data/bump.grf
--------------------------------------------------------------------------
There are not enough slots available in the system to satisfy the 4 slots
that were requested by the application:
  ./test_scotch_dgraph_check

Either request fewer slots for your application, or make more slots available
for use.
--------------------------------------------------------------------------
make[2]: *** [Makefile:258: check_scotch_dgraph_check] Error 1
make[2]: Leaving directory '/home/sigvald/Downloads/scotch/src/scotch_6.0.4/src/check'
make[1]: *** [Makefile:68: ptcheck] Error 2
make[1]: Leaving directory '/home/sigvald/Downloads/scotch/src/scotch_6.0.4/src/check'
make: *** [Makefile:106: ptcheck] Error 2
==> ERROR: A failure occurred in check().
    Aborting...

I find this a bit strange since I don't normally have any problem running mpirun with 4 processes.

ioquatix commented on 2018-02-19 12:38

I get the same problem now. Is there something wrong with the SSL on that website?

sigvald commented on 2018-02-19 12:32

I get the following:

==> Making package: scotch 6.0.4-3 (Mon Feb 19 13:31:18 CET 2018)
==> Checking runtime dependencies...
==> Checking buildtime dependencies...
==> Retrieving sources...
  -> Downloading scotch_6.0.4.tar.gz...
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100   360  100   360    0     0   1592      0 --:--:-- --:--:-- --:--:--  1592
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
curl: (60) SSL certificate problem: unable to get local issuer certificate
More details here: <https://curl.haxx.se/docs/sslcerts.html>

curl failed to verify the legitimacy of the server and therefore could not
establish a secure connection to it. To learn more about this situation and
how to fix it, please visit the web page mentioned above.
==> ERROR: Failure while downloading <http://gforge.inria.fr/frs/download.php/file/34618/scotch_6.0.4.tar.gz>
    Aborting...

zoidberg commented on 2018-01-07 08:03

I am unable to build this package on an up-to-date Arch system. I have pasted the last few lines of the build output below.

make[2]: Entering directory '/home/kishore/.cache/pacaur/scotch/src/scotch_6.0.4/src/check'
gcc -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong -fno-plt -fPIC -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_FILE_COMPRESS_BZ2 -DCOMMON_PTHREAD -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME  -Drestrict=__restrict -DIDXSIZE64 -I../../include -L../../lib test_common_random.c -o test_common_random -lscotch -lscotcherrexit -lz -lbz2 -lm -lrt -pthread
gcc -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong -fno-plt -fPIC -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_FILE_COMPRESS_BZ2 -DCOMMON_PTHREAD -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME  -Drestrict=__restrict -DIDXSIZE64 -I../../include -L../../lib test_common_thread.c -o test_common_thread -lscotch -lscotcherrexit -lz -lbz2 -lm -lrt -pthread
gcc -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong -fno-plt -fPIC -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_FILE_COMPRESS_BZ2 -DCOMMON_PTHREAD -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME  -Drestrict=__restrict -DIDXSIZE64 -I../../include -L../../lib test_strat_seq.c -o test_strat_seq -lscotch -lscotcherrexit -lz -lbz2 -lm -lrt -pthread
gcc -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong -fno-plt -fPIC -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_FILE_COMPRESS_BZ2 -DCOMMON_PTHREAD -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME  -Drestrict=__restrict -DIDXSIZE64 -I../../include -L../../lib test_scotch_graph_coarsen.c -o test_scotch_graph_coarsen -lscotch -lscotcherrexit -lz -lbz2 -lm -lrt -pthread
gcc -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong -fno-plt -fPIC -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_FILE_COMPRESS_BZ2 -DCOMMON_PTHREAD -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME  -Drestrict=__restrict -DIDXSIZE64 -I../../include -L../../lib test_scotch_graph_coarsen_build.c -o test_scotch_graph_coarsen_build -lscotch -lscotcherrexit -lz -lbz2 -lm -lrt -pthread
gcc -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong -fno-plt -fPIC -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_FILE_COMPRESS_BZ2 -DCOMMON_PTHREAD -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME  -Drestrict=__restrict -DIDXSIZE64 -I../../include -L../../lib test_scotch_graph_color.c -o test_scotch_graph_color -lscotch -lscotcherrexit -lz -lbz2 -lm -lrt -pthread
gcc -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong -fno-plt -fPIC -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_FILE_COMPRESS_BZ2 -DCOMMON_PTHREAD -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME  -Drestrict=__restrict -DIDXSIZE64 -I../../include -L../../lib test_scotch_graph_map.c -o test_scotch_graph_map -lscotch -lscotcherrexit -lz -lbz2 -lm -lrt -pthread
gcc -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong -fno-plt -fPIC -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_FILE_COMPRESS_BZ2 -DCOMMON_PTHREAD -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME  -Drestrict=__restrict -DIDXSIZE64 -I../../include -L../../lib test_scotch_graph_map_copy.c -o test_scotch_graph_map_copy -lscotch -lscotcherrexit -lz -lbz2 -lm -lrt -pthread
gcc -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong -fno-plt -fPIC -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_FILE_COMPRESS_BZ2 -DCOMMON_PTHREAD -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME  -Drestrict=__restrict -DIDXSIZE64 -I../../include -L../../lib test_scotch_graph_order.c -o test_scotch_graph_order -lscotch -lscotcherrexit -lz -lbz2 -lm -lrt -pthread
gcc -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong -fno-plt -fPIC -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_FILE_COMPRESS_BZ2 -DCOMMON_PTHREAD -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME  -Drestrict=__restrict -DIDXSIZE64 -I../../include -L../../lib test_scotch_graph_part_ovl.c -o test_scotch_graph_part_ovl -lscotch -lscotcherrexit -lz -lbz2 -lm -lrt -pthread
../../bin/gord data/bump.grf /dev/null -vt
../../bin/gord: symbol lookup error: ../../bin/gord: undefined symbol: fileBlockInit
make[2]: *** [Makefile:152: check_prog_gord] Error 127
make[2]: *** Waiting for unfinished jobs....
make[2]: Leaving directory '/home/kishore/.cache/pacaur/scotch/src/scotch_6.0.4/src/check'
make[1]: *** [Makefile:65: check] Error 2
make[1]: Leaving directory '/home/kishore/.cache/pacaur/scotch/src/scotch_6.0.4/src/check'
make: *** [Makefile:103: check] Error 2
==> ERROR: A failure occurred in check().
    Aborting...

AsmundEr commented on 2017-04-04 06:53

Further investigation revealed this was just me being stupid and running out of space in /tmp, so the check() function couldn't create /tmp/rand.dat. Sorry about the noise, everything seems to work fine now.

ioquatix commented on 2017-04-03 11:30

Can you try cloning the repo for this package and building somewhere other than tmp?

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