I am trying to install Spack on an HPC by following the tutorial:
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%[email protected]~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 '[email protected]'
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 "[email protected]: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%[email protected]~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 errorsPossibly some useful information: In /usr/bin/ I have the following versions of python:
