Spack Installation Errors

Question

I am trying to install Spack on an HPC by following the tutorial:

Installing Spack

I can clone it from GitHub, but when I try to load the environment by inputting:

. share/spack/setup-env.sh

I get the error below (sorry for the poor formatting). I have also tried installing hdf5 but I get a similar error. Is there something that I am missing or should I contact the technicians who maintain the cluster? Thank you for all the help

Spack requires Python 2.7 or 3.5 or higher You are running spack with Python 3.4.10.

From there, I tried changing line 333 in setup-env.sh from:

for cmd in "${SPACK_PYTHON:-}" python3 python python2; do 

to

for cmd in "${SPACK_PYTHON:-}" python2; do

This changes the version of python to the correct one such that when I do:

echo $SPACK_PYTHON
     /usr/bin/python2
/usr/bin/python2 --version
     Python 2.7.18

Finally I try continuing the tutorial inputting:

spack install lib

and I got the following error:

spack install zlib
  ==
  > Bootstrapping clingo from pre - built binaries ==
  > Fetching https: //mirror.spack.io/bootstrap/github-actions/v0.2/build_cache/linux-rhel5-x86_64-gcc-9.3.0-clingo-bootstrap-spack-gypv5loj2ml73duq6sr76yg5rj25te2m.spec.json
  ==
  > Fetching https: //mirror.spack.io/bootstrap/github-actions/v0.2/build_cache/linux-rhel5-x86_64/gcc-9.3.0/clingo-bootstrap-spack/linux-rhel5-x86_64-gcc-9.3.0-clingo-bootstrap-spack-gypv5loj2ml73duq6sr76yg5rj25te2m.spack
  ==
  > Installing "clingo-bootstrap@spack%gcc@9.3.0~docs~ipo+python+static_libstdcpp build_type=Release arch=linux-rhel5-x86_64"
from a buildcache
  ==
  > Bootstrapping patchelf from pre - built binaries ==
  > Bootstrapping patchelf @0 .13 .1: 0.13 .99 % gcc target = x86_64 from sources ==
  > Installing patchelf - 0.13 .1 - ryv6d2pumi2fhaqoetncdofvtkliz2ry ==
  > No binary
for patchelf - 0.13 .1 - ryv6d2pumi2fhaqoetncdofvtkliz2ry found: installing from source ==
  > Using cached archive: /ddn/home
1 / r3031 / software / spack /
  var / spack / cache / _source - cache / archive / 08 / 08 c0237e89be74d61ddf8f6ff218439cdd62af572d568fb38913b53e222831de.tar.gz ==
  > No patches needed
for patchelf
  ==
  > patchelf: Executing phase: 'autoreconf' ==
  > patchelf: Executing phase: 'configure' ==
  > patchelf: Executing phase: 'build' ==
  > Error: ProcessError: Command exited with status 2:
  'make'
'-j16'
'V=1'

4 errors found in build log:
  36 Making all in src
37 make[1]: Entering directory '/tmp/r3031/spack-stage/spack-stage-patchelf-0.13.1-ryv6d2pumi2fhaqoetncdofvtkliz2ry/spack-src/src'
38 source = 'patchelf.cc'
object = 'patchelf.o'
libtool = no\
39 DEPDIR = .deps depmode = none / bin / sh.. / build - aux / depcomp\
40 g++ - DPACKAGE_NAME = \"patchelf\" -DPACKAGE_TARNAME=\"patchelf\" -DPACKAGE_VERSION=\"0.13.1.20211127.72b6d44\" -DPACKAGE_STRING=\"patchelf\ 0.13.1.202
11127.72 b6d44\ " -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"patchelf\" -DVERSION=\"0.13.1.20211127.72b6d44\" -I.    -Wall -std=c++11 -D_
FILE_OFFSET_BITS = 64 - c - o patchelf.o patchelf.cc
41[spack cc] ERROR: Compiler 'gcc@4.8'
does not have a C++compiler configured. >>
  42 Makefile: 366: recipe
for target 'patchelf.o'
failed
  >>
  43 make[1]: ** * [patchelf.o] Error 1
44 make[1]: Leaving directory '/tmp/r3031/spack-stage/spack-stage-patchelf-0.13.1-ryv6d2pumi2fhaqoetncdofvtkliz2ry/spack-src/src' >>
  45 Makefile: 439: recipe
for target 'all-recursive'
failed
  >>
  46 make: ** * [all - recursive] Error 1

See build log
for details:
  /tmp/r
3031 / spack - stage / spack - stage - patchelf - 0.13 .1 - ryv6d2pumi2fhaqoetncdofvtkliz2ry / spack - build - out.txt

  ==
  > Bootstrapping clingo from sources ==
  > Error: cannot bootstrap the "clingo"
Python module from spec "clingo-bootstrap@spack+python %gcc target=x86_64"
due to the following failures:
  github - actions - v0 .2 raised RuntimeError: cannot bootstrap any of the patchelf executables from spec "patchelf@0.13.1:0.13.99 %gcc target=x86_64"
due to the following failures:
  github - actions - v0 .2 raised IOError: [Errno 2] No such file or directory: '/ddn/home1/r3031/software/spack/share/spack/bootstrap/github-actions-v0.2/patchelf.json'
github - actions - v0 .1 raised ValueError: source is not trusted
spack - install raised ChildError: ProcessError: Command exited with status 2:
  'make'
'-j16'
'V=1'
Run `spack --debug ...`
for more detailed errors
github - actions - v0 .1 raised ValueError: source is not trusted
spack - install raised ConflictsInSpecError: Conflicts in concretized spec "clingo-bootstrap@spack%gcc@4.8~docs~ipo+python~static_libstdcpp build_type=Release arch=linux-sle_hpc12-x86_64/brcc7l3"

List of matching conflicts
for spec:

  clingo - bootstrap @spack % gcc @4 .8~docs~ipo + python~static_libstdcpp build_type = Release arch = linux - sle_hpc12 - x86_64 ^
  bison @2 .7 % gcc @4 .8 arch = linux - sle_hpc12 - x86_64 ^
  cmake @3 .23 .1 % gcc @4 .8~doc + ncurses + ownlibs~qt build_type = Release arch = linux - sle_hpc12 - x86_64 ^
  ncurses @6 .2 % gcc @4 .8~symlinks + termlib abi = none arch = linux - sle_hpc12 - x86_64 ^
  pkgconf @1 .8 .0 % gcc @4 .8 arch = linux - sle_hpc12 - x86_64 ^
  openssl @1 .1 .1 o % gcc @4 .8~docs~shared certs = system arch = linux - sle_hpc12 - x86_64 ^
  perl @5 .34 .1 % gcc @4 .8 + cpanm + shared + threads arch = linux - sle_hpc12 - x86_64 ^
  berkeley - db @18 .1 .40 % gcc @4 .8 + cxx~docs + stl patches = b231fcc arch = linux - sle_hpc12 - x86_64 ^
  bzip2 @1 .0 .8 % gcc @4 .8~debug~pic + shared arch = linux - sle_hpc12 - x86_64 ^
  diffutils @3 .8 % gcc @4 .8 arch = linux - sle_hpc12 - x86_64 ^
  libiconv @1 .16 % gcc @4 .8 libs = shared, static arch = linux - sle_hpc12 - x86_64 ^
  gdbm @1 .19 % gcc @4 .8 arch = linux - sle_hpc12 - x86_64 ^
  readline @8 .1 % gcc @4 .8 arch = linux - sle_hpc12 - x86_64 ^
  zlib @1 .2 .12 % gcc @4 .8 + optimize + pic + shared patches = 0 d38234 arch = linux - sle_hpc12 - x86_64 ^
  python @2 .7 % gcc @4 .8 + bz2 + ctypes + dbm~debug + ensurepip + libxml2~nis~optimizations + pic + pyexpat + pythoncmd + readline + shared + sqlite3 + ssl~tix~tkinter + ucs4 + uuid + zlib arch = linux - sle_hpc12 - x86_64 ^
  re2c @2 .2 % gcc @4 .8 arch = linux - sle_hpc12 - x86_64

1. "%gcc@:5"
conflicts with "clingo-bootstrap" [C++14 support is required to bootstrap clingo]

Run `spack --debug ...`
for more detailed errors

---

Possibly some useful information: In /usr/bin/ I have the following versions of python:

Answer 1

I don't see any question here, so trying to leave a couple of tips.

The first one is that you don't need to hack the shell script to force the version of Python. You can simply:

export SPACK_PYTHON=<python-you-want-to-use>

For instance, you can point Spack to use the Python 3.6 interpreter you seem to have on the machine.

The second tip is that you can use the following Docker image:

$ docker pull ghcr.io/spack/tutorial:latest

to go through the tutorial on e.g. your own laptop instead of the HPC cluster you got access to. This will give you time to familiarize with Spack before using it on the cluster.

Hope that helps.