p.p.s. Just to be sure, i wiped my installations of Spack on Ubuntu16.04+gcc5.4.0 PC and Centos7+gcc4.8.5 cluster and reinstalled everything from scratch using commit 1124bdc99ee84c26201c40536d9b04dac74d7f6a (this is the current HEAD in Spack, I updated dealii's wiki to mention it).
I still think it's good to report cluster-specific issues on Spack's github page so that they are (eventually) fixed. Regards, Denis. On Thursday, March 16, 2017 at 6:43:13 PM UTC+1, Bruno Turcksin wrote: > > Steve, > > I have tried to use spack several times on two clusters and it never > worked for me (but it works fine on my own machine). I usually have to > patch a bunch of things and at the end, I still have problems when I load > the modules. I find it a lot easier to install everything manually. You can > also try candi, there is an option to build deal.II on a cluster. > > Best, > > Bruno > > On Thursday, March 16, 2017 at 12:19:36 PM UTC-4, Stephen DeWitt wrote: >> >> Hello, >> I'm trying to install dealii on a shared AFS file system. Originally, I >> tried to install everything manually, which I had done successfully on our >> HPC cluster, but ran into a PETSc link error and decided to try Spack. >> >> I followed the instructions on the deal.II wiki, but installation stopped >> during the "install" phase for "ncurses". The packages "bzip2" and >> "muparser" installed without a problem. >> >> Here's the error message: >> >> ######################################################################## >> 100.0% >> >> *==>* Staging archive: /afs/ >> umich.edu/user/s/t/stvdwtt/Public/PRISMS/software/spack/spack/var/spack/stage/ncurses-6.0-4wkexyzgaxdwrfs6wqje2ppcm5di263m/ncurses-6.0.tar.gz >> >> *==>* Created stage in /afs/ >> umich.edu/user/s/t/stvdwtt/Public/PRISMS/software/spack/spack/var/spack/stage/ncurses-6.0-4wkexyzgaxdwrfs6wqje2ppcm5di263m >> >> *==>* Applied patch sed_pgi.patch >> >> *==>* Ran patch() for ncurses >> >> *==>* Building ncurses [AutotoolsPackage] >> >> *==>* Executing phase : 'autoreconf' >> >> *==>* Executing phase : 'configure' >> >> *==>* Executing phase : 'build' >> >> *==>* Executing phase : 'install' >> >> *==>* Error: ProcessError: Command exited with status 2: >> >> 'make' '-j2' 'install' >> >> /afs/ >> umich.edu/user/s/t/stvdwtt/Public/PRISMS/software/spack/spack/lib/spack/spack/build_systems/autotools.py:282, >> >> in install: >> >> 277 def install(self, spec, prefix): >> >> 278 """Makes the install targets specified by >> >> 279 :py:attr:``~.AutotoolsPackage.install_targets`` >> >> 280 """ >> >> 281 with working_dir(self.build_directory): >> >> >> 282 inspect.getmodule(self).make(*self.install_targets) >> >> >> See build log for details: >> >> /tmp/stvdwtt/spack-stage/spack-stage-7oak9b/ncurses-6.0/spack-build.out >> >> I went to the build log (which is quite long), and see several errors >> like this: >> >> cd ../lib && (ln -s -f libpanel.so.6.0 libpanel.so.6; ln -s -f >> libpanel.so.6 libpanel.so; ) >> >> /usr/bin/ld: total time in link: 0.021996 >> >> /usr/bin/ld: data size 29224512 >> >> cd /afs/ >> umich.edu/user/s/t/stvdwtt/Public/PRISMS/software/spack/spack/opt/spack/linux-rhel6-x86_64/gcc-4.4.7/ncurses-6.0-4wkexyzgaxdwrfs6wqje2ppcm5di263m/lib >> >> && (ln -s -f libpanel.so.6.0 libpanel.so.6; ln -s -f libpanel.so.6 >> libpanel.so; ) >> >> test -z "" && /sbin/ldconfig >> >> /sbin/ldconfig: Can't create temporary cache file /etc/ld.so.cache~: >> Permission denied >> >> make[1]: [/afs/ >> umich.edu/user/s/t/stvdwtt/Public/PRISMS/software/spack/spack/opt/spack/linux-rhel6-x86_64/gcc-4.4.7/ncurses-6.0-4wkexyzgaxdwrfs6wqje2ppcm5di263m/lib/libpanel.so.6.0] >> >> Error 1 (ignored) >> >> The last few lines of the build log (which I'm not sure are relevant) are: >> >> Running sh /afs/ >> umich.edu/user/s/t/stvdwtt/Public/PRISMS/software/spack/spack/var/spack/stage/ncurses-6.0-4wkexyzgaxdwrfs6wqje2ppcm5di263m/ncurses-6.0/misc/shlib >> >> tic to install /afs/ >> umich.edu/user/s/t/stvdwtt/Public/PRISMS/software/spack/spack/opt/spack/linux-rhel6-x86_64/gcc-4.4.7/ncurses-6.0-4wkexyzgaxdwrfs6wqje2ppcm5di263m/share/terminfo >> >> ... >> >> >> You may see messages regarding extended capabilities, e.g., AX. >> >> These are extended terminal capabilities which are compiled >> >> using >> >> tic -x >> >> If you have ncurses 4.2 applications, you should read the INSTALL >> >> document, and install the terminfo without the -x option. >> >> >> ** creating form.pc >> >> ** creating ncurses++.pc >> >> touch pc-files >> >> /bin/sh -c 'for name in *.pc; do /usr/bin/install -c -m 644 $name /afs/ >> umich.edu/user/s/t/stvdwtt/Public/PRISMS/software/spack/spack/opt/spack/linux-rhel6-x86_64/gcc-4.4.7/ncurses-6.0-4wkexyzgaxdwrfs6wqje2ppcm5di263m/lib/pkgconfig/$name; >> >> done' >> >> Judging from the error, I'm assuming that it's a permissions issue. I >> double-checked that my $SPACK_ROOT environment variable is set correctly. >> The first line of the build log includes a '--prefix=' statement, which >> correctly picks up the $SPACK_ROOT path. >> >> Does anyone have ideas on what the problem is? Digging around the Spack >> documentation didn't turn up anything. >> >> Thanks! >> Steve >> > -- The deal.II project is located at http://www.dealii.org/ For mailing list/forum options, see https://groups.google.com/d/forum/dealii?hl=en --- You received this message because you are subscribed to the Google Groups "deal.II User Group" group. To unsubscribe from this group and stop receiving emails from it, send an email to dealii+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout.
