Installation using Spack fails during 'ncurses' installation

[Stephen DeWitt]

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

[Bruno Turcksin]

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

[Jean-Paul Pelteret]

Dear Stephen,

Since this is an issue related not directly to deal.II but rather Spack itself (ncurses is only a dependency of a dealii related package), I would suggest that you post your question on their forum. You'll generally get a quick response there, and if not then you should open an issue on their github page.

Best regards,

Jean-Paul

[Denis Davydov]

@Stephen DeWitt 

I think the best place to report such problems is https://github.com/LLNL/spack/issues

Looking at your error, i think it happens within your cluster, as it's ldconfig which complains

/sbin/ldconfig: Can't create temporary cache file /etc/ld.so.cache~: Permission denied

But frankly, i have no idea what is going on. 

If you have ncurses provided by your OS and it has a standard prefix/include with prefix/lib or prefix/lib64 locations,

then you can try using it instead by adding to your ~/.spack/linux/packages.yaml`

packages:
  ncurses:
    version: [6.0]
    paths:
      ncrses@6.0%g...@4.8.5: /path/to/ncurses/prefix/
    buildable: False

which will instruct Spack that this package is provided externally and there is no need to build it.

There are plans to add OS specific configuration scopes to automate usage of external packages, but it's not yet there,

see https://github.com/LLNL/spack/issues/2700

@Bruno

On Thursday, March 16, 2017 at 6:43:13 PM UTC+1, Bruno Turcksin wrote:

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

I am sorry, but when I see those comments, I have to say that I use Spack all the time on our cluster and it works for me. 

And it does for other folks in our chair who use it on the same cluster for their calculations with deal.II. 

Not only that, it works on my macOS Sierra and on a PC with Ubuntu 16.04. Bottom line - YMMW.

Regards,

Denis.

[Denis Davydov]

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 

p.s. maybe a good idea is to report what does not work here https://github.com/LLNL/spack/issues ?.. 

[Denis Davydov]

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:

[Stephen DeWitt]

Bruno, Jean-Paul, and Denis,

Thank you all for your responses. As suggested, I'll send a message to the Spack forum and/or open an issue on their GitHub site. In the meantime, I'll continue debugging the manual PETSc installation to see if I can get that to work. I think the filesystem I'm trying to install this to is a bit of an edge case in that I neither have root access nor are there many useful libraries preinstalled.

@Denis,

Thanks for taking the time to redo your Spack installations, I appreciate it. 

I want close saying that I appreciate the effort you have put into making deal.II easy/easier to install, between the Mac packages, Spack, candi (although, unfortunately, I haven't had much luck with that either), and all of the detailed installation documentation.

Thanks,

Steve