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Spack is a moving target and receives multiple commits per day. Normally, HPCToolkit will build and run successfully with the latest version of all of its prerequisite packages, but sometimes not. This page covers the current known issues where HPCToolkit fails to build with the latest version of spack. The main build directions are at:
Report problems to hpctoolkit-forum at rice dot edu. But before
reporting a problem, first try the versions recommended in the
packages.yaml file in the spack subdirectory of the
hpctoolkit repository. And always check the latest version of this file
on the hpctoolkit web site.
Last revised: September 11, 2020.
As of commit
b2d3d067ecad
on 2020-09-05, the master branch now wants libunwind and xz (lzma) to
be built with variant +pic. This is used to workaround a
deadlock with hpcrun, openmpi 4.x and UCX. If not, then you’ll see
this warning at the bottom of configure.
WARNING: The following prereqs are missing an archive (.a) compiled with -fPIC. WARNING: libunwind lzma WARNING: WARNING: hpcrun is unable to properly hide these libraries from the WARNING: application and this may cause deadlock or segfault. WARNING: Recompile the above libraries with -fPIC (+pic in spack).
For now, this is only a warning. Everything will work as before, you
just won’t get the benefit of the work around. But going forward, you
should build libunwind and xz with variant +pic. For example,
in packages.yaml.
libunwind: version: [1.4.0] variants: +xz +pic xz: version: [5.2.5] variants: +pic
Spack compiler find was previously broken for detecting the
front-end compilers on Cray that HPCToolkit uses.
Fixed: This is now fixed in commit 789d060ff61b on 2020-06-29.
Note: Remember, you still need to fill in the modules:
field with the following four modules. For example, this is an entry
for the gcc/8.3.0 module on theta at ANL. Note that the
front-end operating_system is something like sles15 (not
cnl6), and the front-end target is x86_64 (not
mic_knl). Your versions may differ.
- compiler:
environment: {}
flags: {}
modules:
- PrgEnv-gnu/6.0.7
- gcc/8.3.0
- craype/2.6.5
- cray-mpich/7.7.14
operating_system: sles15
paths:
cc: /opt/gcc/8.3.0/bin/gcc
cxx: /opt/gcc/8.3.0/bin/g++
f77: /opt/gcc/8.3.0/bin/gfortran
fc: /opt/gcc/8.3.0/bin/gfortran
spec: gcc@8.3.0
target: x86_64
These are general problems that arise from time to time.
Sometimes spack fails to download the source file(s) for some package and dies with a message similar to this.
==> Fetching from https://ftpmirror.gnu.org/m4/m4-1.4.18.tar.gz failed. ==> Error: FetchError: All fetchers failed for m4-1.4.18-vorbvkcjfac43b7vuswsvnm6xe7w7or5
This problem is usually temporary and the solution is to either wait a few minutes or an hour and try again, or else download the file manually and put it into a spack mirror.
Another way fetch can fail is with a connection timeout. Some sites,
especially sourceforge are often slow to connect. If this happens, then
increase the connection timeout in config.yaml to 30 or 60
seconds (default is 10 seconds).
Sometimes the latest version of some package breaks the build. This has happened a couple of times where a new version of Boost has broken the build for Dyninst. The solution is to revert the package to an earlier version until the rest of the code catches up.
Sometimes but rarely, something in the spack core will change or break
the code in some package.py file. The solution is to look
through the spack git log and revert the repository to a recent commit
before the breakage.
Avoid boost version 1.68.0, it breaks the build for hpctoolkit. Version 1.70.0 works with the latest version of dyninst (10.1.0), or else 1.66.0 is good and works with all versions of dyninst.
Elfutils 0.176 requires glibc 2.16 or later (for aligned_alloc)
and won’t work with an older glibc, including RedHat or CentOS 6.x and
Blue Gene. On systems with an old glibc, use version 0.175.
IBM is fairly aggressive about taking down old versions, so you may find that fetching ibm-java fails while trying to install hpcviewer (powerpc only).
==> Installing ibm-java ==> No binary for ibm-java found: installing from source ==> Error: FetchError: All fetchers failed
If this happens, first compare spack info ibm-java with what
versions are available at IBM’s download site. If there is another
8.0.x.y version that spack understands that is still available for
download, then use that.
If not, then manually download the latest 8.0.x.y version, compute a
sha256sum checksum for the file and then edit the
ibm-java/package.py file to add this version. And then report
the problem to the spack maintainer.