install CP2K with spack
May Abdelghani
Gamblin, Todd
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Pariksheet Nanda
Try concretizing with the openmp for the fftw and openblas dependencies as suggested by the bottom 2 errors:
spack spec cp2k ^fftw+openmp ^openblas threads=openmp
... though I concede your point that it's odd that the vanilla `spack spec cp2k` produces those errors using:
$ spack debug report
* **Spack:** 0.16.1-2662-379a1fd23b
* **Python:** 3.7.3
* **Platform:** linux-debian10-nehalem
* **Concretizer:** original
I'm not seeing a GitHub issue about this particular cp2k bug or
feature, but then again, I actually don't know if it's sane
behavior for spack to automagically flip flags from the defaults
on dependent packages, or if spack relies on the user to make
those sorts of decisions, or whether flipping dependency flags is
made difficult by the limited backtracking of the original
concretizer - maybe someone can comment about this.
*Message sent from a system outside of UConn.*
Pariksheet Nanda
Hello,
Sorry to hear that you're still running into difficulties
installing cp2k@7.1. It's a little difficult to comment about the
libxsmm obstacle you ran into because you didn't supply any
information about the error(s) you're seeing. You're using Centos
7 SandyBridge and libxsmm has some CPU architecture specific
behaviors. Would you be able to file a new issue about the
libxsmm error you are seeing on GitHub
https://github.com/spack/spack/issues?
It's worth noting that you can choose to use another library for small matrix multiplications (smm) by changing an option to cp2k to workaround the error with libxsmm. From looking at `spack info cp2k` you can see that the smm variant allows libxsmm, libsmm or blas. Because openblas is already being pulled in as a dependency and it's generally quite fast, perhaps it makes sense to reuse that dependency:
spack spec cp2k smm=blas ^fftw+openmp ^openblas threads=openmp
Additionally I see a comment in the cp2k package.py that also
suggests using smm=blas for compiling on aarch64.
Let us know how you get along!
Pariksheet
*Message sent from a system outside of UConn.*
Hello,
Well, everything worked fine when using the “spack install cp2k@7.1 ^fftw+openmp ^openblas threads=openmp” command, but new obstacles appeared during the installation of “libxsmm-1.16.1-rmhl6r25mydfwhed4ckwsyu5b6xw4yss.I will try to overcome these problems, and if I cannot solve these issues on my own, I will present them for discussion in this group ... Thank you very much.
To view this discussion on the web visit https://groups.google.com/d/msgid/spack/e6472a9d-a0c4-2907-2639-2a7315412d80%40uconn.edu.
Pariksheet Nanda
FYI
-------- Forwarded Message --------
| Subject: | Re: [spack] install CP2K with spack |
|---|---|
| Resent-From: | parikshe...@uconn.edu |
| Date: | Mon, 17 May 2021 20:27:38 +0000 (UTC) |
| From: | may abdelghani <may...@gmail.com> |
| Reply-To: | may abdelghani <may...@gmail.com> |
| To: | Pariksheet Nanda <parikshe...@uconn.edu> |
My thanks and appreciation to those who have made this process successful.
I think I found where the issue comes from. The line 11290 below right before the error comes from these lines in file ./spack-src/generated/fortran/Makefile:
libint2_types_f.h: $(TOPDIR)/include/libint2.h.i
$(PYTHON) c_to_f.py $< $@ Libint_t
But in your case for some reason spack is setting
PYTHON as /home/may/xtb/python/ during configure
time. If I check my libint config.log, my
PYTHON='python' per below:
$ spack cd -b libint +fortran tune=cp2k-lmax-5
$ grep python config.log
configure:5228: checking for python
configure:5244: found /usr/bin/python
configure:5255: result: python
ac_cv_prog_PYTHON=python
PYTHON='python'
So it would be interesting to know what your config.log looks like. Per configure.ac it looks for programs named either of: python python3 python2 python2.7
Do you have a python module on your cluster you can load, and then re-run your command to install cp2k? Either python version 2.7 or any version 3 seems like it should work.
In the worst case, libint is a non-essential part of cp2k and if you don't need it for your work, you can disable it with ~libint like so:
spack install cp2k ~libint smm=blas ^fftw+openmp
^openblas threads=openmp
Pariksheet
Hello,
I am sorry to say, Pariksheet Nanda, there has been a small improvement.
When I typed:
spack spec cp2k smm=blas ^fftw+openmp ^openblas threads=openmp,
I got the lines below (=the installation has not yet been completed).
also, the file spack-build-out.txt is attached.
[+]
/home/may/spack/opt/spack/linux-centos7-sandybridge/gcc-8.3.0/libsigsegv-2.12-mkcsdp6t2vrvuermpvsmoqxzvuythaw2
[+]
/home/may/spack/opt/spack/linux-centos7-sandybridge/gcc-8.3.0/pkgconf-1.7.3-bnbddzydzrhptjopktsnnd7525pm3xjc
[+]
/home/may/spack/opt/spack/linux-centos7-sandybridge/gcc-8.3.0/util-macros-1.19.1-dgwrf2rhls3yvramq2zphczy6iqu4xxi
[+]
/home/may/spack/opt/spack/linux-centos7-sandybridge/gcc-8.3.0/libiconv-1.16-c2xcb2qlur7jopdhowguoyxee7ztw7ls
[+]
/home/may/spack/opt/spack/linux-centos7-sandybridge/gcc-8.3.0/xz-5.2.5-6s6ge4esew4bntyia7kpzdlqobmwrmwn
[+]
/home/may/spack/opt/spack/linux-centos7-sandybridge/gcc-8.3.0/zlib-1.2.11-gvqgapfrjasckctvhozcfn2c3yfxcx7l
[+]
/home/may/spack/opt/spack/linux-centos7-sandybridge/gcc-8.3.0/berkeley-db-18.1.40-t3oevvtiunac4mfdtjqhaxb2jrqidrqm
[+]
/home/may/spack/opt/spack/linux-centos7-sandybridge/gcc-8.3.0/libxc-4.3.4-zclfwde7ozjudj3sx27zlrulmfcnibmb
[+]
/home/may/spack/opt/spack/linux-centos7-sandybridge/gcc-8.3.0/openblas-0.3.12-tbmsk7c5pdknbrbrgrevhnd5nk72eypw
[+]
/home/may/spack/opt/spack/linux-centos7-sandybridge/gcc-8.3.0/libbsd-0.10.0-txucv7q2zpvqubt5we4a7xdvlyhjtw2m
[+]
/home/may/spack/opt/spack/linux-centos7-sandybridge/gcc-8.3.0/libffi-3.3-4kme6rlfwcjcq5ip5qymqifwxpbdx4sc
[+]
/home/may/spack/opt/spack/linux-centos7-sandybridge/gcc-8.3.0/libuuid-1.0.3-4lgkkxqabofmizkdpmro2lbew3wy7ufk
[+]
/home/may/spack/opt/spack/linux-centos7-sandybridge/gcc-8.3.0/m4-1.4.18-53zx5qsvmuxbjxqa34rkvp7wxovvfaas
[+]
/home/may/spack/opt/spack/linux-centos7-sandybridge/gcc-8.3.0/ncurses-6.2-2glicvrvhyxrcmanhx3yq4mw72l7jd7d
[+]
/home/may/spack/opt/spack/linux-centos7-sandybridge/gcc-8.3.0/diffutils-3.7-5n6aocuo5x6nlptzcb2tzjo2yf2cmqig
[+]
/home/may/spack/opt/spack/linux-centos7-sandybridge/gcc-8.3.0/tar-1.32-awi54nmr73qxulsen44vnqy7nqfow662
[+]
/home/may/spack/opt/spack/linux-centos7-sandybridge/gcc-8.3.0/libxml2-2.9.10-skx6344agh5kurxlsezxvdtfnhrrnsq3
[+]
/home/may/spack/opt/spack/linux-centos7-sandybridge/gcc-8.3.0/expat-2.2.10-zkb54ve4ab67h5rjnoxrnhyywcz46qwt
[+]
/home/may/spack/opt/spack/linux-centos7-sandybridge/gcc-8.3.0/libtool-2.4.6-tkj7dwxlqj3siya4ujuljs6phmkp2wui
[+]
/home/may/spack/opt/spack/linux-centos7-sandybridge/gcc-8.3.0/readline-8.0-3ythu4vyatm4szmn2f4cmphg7tuy7sda
[+]
/home/may/spack/opt/spack/linux-centos7-sandybridge/gcc-8.3.0/bzip2-1.0.8-p7ecccxh5bdu6akw6nvcshdvuaq5vyb2
[+]
/home/may/spack/opt/spack/linux-centos7-sandybridge/gcc-8.3.0/libpciaccess-0.16-vsbg7sdqzrnjko7ulaw67rt3kph5uuaa
[+]
/home/may/spack/opt/spack/linux-centos7-sandybridge/gcc-8.3.0/gdbm-1.18.1-pk2krpidpqvsih6dwpfgj3psbi3zbjtv
[+]
/home/may/spack/opt/spack/linux-centos7-sandybridge/gcc-8.3.0/sqlite-3.33.0-esaqnljw5uta4fw3sbt4j6gfevxyy26g
[+]
/home/may/spack/opt/spack/linux-centos7-sandybridge/gcc-8.3.0/boost-1.74.0-gh625p7lfpahdymaiae7qo3jyjpuyf5s
[+]
/home/may/spack/opt/spack/linux-centos7-sandybridge/gcc-8.3.0/gettext-0.21-t3ky2kdejhhdyzdb3ix24ctwpi3c5q6v
[+]
/home/may/spack/opt/spack/linux-centos7-sandybridge/gcc-8.3.0/perl-5.32.0-s2v2fshtbgykzwxh22q7dvpmnoqoigri
[+]
/home/may/spack/opt/spack/linux-centos7-sandybridge/gcc-8.3.0/openssl-1.1.1h-te2gtu7hjdhfsotq3ezbtty5sl5jr77k
[+]
/home/may/spack/opt/spack/linux-centos7-sandybridge/gcc-8.3.0/autoconf-2.69-cq62hjvnjclczsqkn3mykvokse356jjs
[+]
/home/may/spack/opt/spack/linux-centos7-sandybridge/gcc-8.3.0/cmake-3.18.4-pwgi32je2miodrln35ifw6gcclefhc4k
[+]
/home/may/spack/opt/spack/linux-centos7-sandybridge/gcc-8.3.0/python-3.8.6-6lihbqt6xj7iwiygvlrk5lxkrbwmjmmm
[+]
/home/may/spack/opt/spack/linux-centos7-sandybridge/gcc-8.3.0/automake-1.16.2-5rkykquanv5gd6pu4tgodtj3i4pq4o6q
[+]
/home/may/spack/opt/spack/linux-centos7-sandybridge/gcc-8.3.0/numactl-2.0.14-wdm3jewxm7ov74iqxswdx2e6htad2ocd
[+]
/home/may/spack/opt/spack/linux-centos7-sandybridge/gcc-8.3.0/gmp-6.1.2-gyma62f4mqbfyyog3arogajakdmhhvcf
[+]
/home/may/spack/opt/spack/linux-centos7-sandybridge/gcc-8.3.0/hwloc-1.11.11-6b6iuz4gbdunptuoxbvaa2de5qqurk3f
==>
Installing
libint-2.6.0-r7fwx6dcffiv23atpqbj2vl52qaxixy5
==> No binary for
libint-2.6.0-r7fwx6dcffiv23atpqbj2vl52qaxixy5
found: installing from source
==> Using cached archive:
/home/may/spack/var/spack/cache/_source-cache/archive/4a/4ae47e8f0b5632c3d2a956469a7920896708e9f0e396ec10071b8181e4c8d9fa.tar.gz
==> libint: Executing phase:
'autoreconf'
==> libint: Executing phase:
'configure'
==> libint: Executing phase: 'build'
==> libint: Executing phase: 'install'
==> Error: ProcessError: Command exited
with status 2:
'make' '-j16' 'install'
3 errors found in build log:
11285 /usr/bin/install -c -m 0644
/tmp/may/spack-stage/spack-stage-libint-2.6.0
-r7fwx6dcffiv23atpqbj2vl52qaxixy5/spack-src/generated/./include/libint2/*
.h
/home/may/spack/opt/spack/linux-centos7-sandybridge/gcc-8.3.0/libint-2
.6.0-r7fwx6dcffiv23atpqbj2vl52qaxixy5/include/libint2
11286 make[1]: Entering directory
`/tmp/may/spack-stage/spack-stage-libint-2.6.
0-r7fwx6dcffiv23atpqbj2vl52qaxixy5/spack-src/generated/fortran'
11287 make[1]: warning: jobserver
unavailable: using -j1. Add `+' to parent
ma
ke rule.
11288 /usr/bin/install -c -m 0644
/tmp/may/spack-stage/spack-stage-libint-2.6.0
-r7fwx6dcffiv23atpqbj2vl52qaxixy5/spack-src/generated/./lib/basis/*
/home
/may/spack/opt/spack/linux-centos7-sandybridge/gcc-8.3.0/libint-2.6.0-r7f
wx6dcffiv23atpqbj2vl52qaxixy5/share/libint/2.6.0/basis
11289
/home/may/spack/lib/spack/env/gcc/g++ -E
-DHAVE_CONFIG_H -D__COMPILING_LI
BINT2=1
-D__COMPILING_LIBINT2=1 -I../include
-I..//include -O2 -O2 ../i
nclude/libint2.h >
../include/libint2.h.i
11290 /home/may/xtb/python/:
c_to_f.py ../include/libint2.h.i
libint2_types_f.h
Libint_t
>> 11291 /bin/sh:
/home/may/xtb/python/:: No such file or
directory
>> 11292 make[1]: ***
[libint2_types_f.h] Error 127
11293 make[1]: Leaving directory
`/tmp/may/spack-stage/spack-stage-libint-2.6.0
-r7fwx6dcffiv23atpqbj2vl52qaxixy5/spack-src/generated/fortran'
>> 11294 make: *** [fortran]
Error 1
11295 make: *** Waiting for
unfinished jobs....
11296 /usr/bin/install -c -m 0644
/tmp/may/spack-stage/spack-stage-libint-2.6.0
-r7fwx6dcffiv23atpqbj2vl52qaxixy5/spack-src/generated/./include/libint2_*
.h
/home/may/spack/opt/spack/linux-centos7-sandybridge/gcc-8.3.0/libint-2
.6.0-r7fwx6dcffiv23atpqbj2vl52qaxixy5/include/libint2
11297 /usr/bin/install -c -m 0644
./include/libint2/config.h
/home/may/spack/op
t/spack/linux-centos7-sandybridge/gcc-8.3.0/libint-2.6.0-r7fwx6dcffiv23at
pqbj2vl52qaxixy5/include/libint2
11298 /usr/bin/install -c -d -m
0755
/home/may/spack/opt/spack/linux-centos7-sa
ndybridge/gcc-8.3.0/libint-2.6.0-r7fwx6dcffiv23atpqbj2vl52qaxixy5/include
/libint2/chemistry
11299 /usr/bin/install -c -m 0644
/tmp/may/spack-stage/spack-stage-libint-2.6.0
-r7fwx6dcffiv23atpqbj2vl52qaxixy5/spack-src/generated/./include/libint2/c
hemistry/*.h
/home/may/spack/opt/spack/linux-centos7-sandybridge/gcc-8.3.
0/libint-2.6.0-r7fwx6dcffiv23atpqbj2vl52qaxixy5/include/libint2/chemistry
11300 /usr/bin/install -c -d -m
0755
/home/may/spack/opt/spack/linux-centos7-sa
ndybridge/gcc-8.3.0/libint-2.6.0-r7fwx6dcffiv23atpqbj2vl52qaxixy5/include
/libint2/lcao
See
build log for details:
/tmp/may/spack-stage/spack-stage-libint-2.6.0-r7fwx6dcffiv23atpqbj2vl52qaxixy5/spack-build-out.txt
==>
Warning: Skipping build of
cp2k-7.1-g4d2hqywfb7egen3wjrelhvka5zqux27
since
libint-2.6.0-r7fwx6dcffiv23atpqbj2vl52qaxixy5
failed
[+]
/home/may/spack/opt/spack/linux-centos7-sandybridge/gcc-8.3.0/openmpi-3.1.6-kk42s2oa4e3hk3ctpcnv3gj5rfhujzss
[+]
/home/may/spack/opt/spack/linux-centos7-sandybridge/gcc-8.3.0/fftw-3.3.8-2k34ffzyh63seaqcbprc4tirkrob6ucy
[+]
/home/may/spack/opt/spack/linux-centos7-sandybridge/gcc-8.3.0/netlib-scalapack-2.1.0-5wwa5k7qpajyycxt4jjhlgmn73tzc7mg
Sorry about that! I meant "install", not "spec". Using "spec" shows you what it would install instead of installing for you.
Pariksheet
On 5/16/21 9:05 AM, may abdelghani wrote:
*Message sent from a system outside of UConn.*
well,
When I wrote the command:
spack spec cp2k smm=blas ^fftw+openmp ^openblas threads=openmp
The following data emerged:
--------------------------------
cp2k smm=blas^fftw+openmp^openblas threads=openmp
Concretized--------------------------------cp2k@7.1%g...@8.3.0~cosma~cuda~cuda_arch_35_k20x~cuda_blas~cuda_fft~elpa+libint+libxc+mpi+openmp~pexsi~plumed~sirius cuda_arch=none lmax=5 smm=blas arch=linux-centos7-sandybridge^ff...@3.3.8%g...@8.3.0+mpi+openmp~pfft_patches precision=double,float arch=linux-centos7-sandybridge
^netlib-s...@2.1.0%g...@8.3.0~ipo~pic+shared build_type=Release patches=1c9ce5fee1451a08c2de3cc87f446aeda0b818ebbce4ad0d980ddf2f2a0b2dc4,f2baedde688ffe4c20943c334f580eb298e04d6f35c86b90a1f4e8cb7ae344a2 arch=linux-centos7-sandybridge^cm...@3.18.4%g...@8.3.0~doc+ncurses+openssl+ownlibs~qt patches=bf695e3febb222da2ed94b3beea600650e4318975da90e4a71d6f31a6d5d8c3d arch=linux-centos7-sandybridge
^ope...@1.1.1h%g...@8.3.0+systemcerts arch=linux-centos7-sandybridge^open...@0.3.12%g...@8.3.0~consistent_fpcsr~ilp64+pic+shared threads=openmp arch=linux-centos7-sandybridge
^pyt...@3.8.6%g...@8.3.0+bz2+ctypes+dbm~debug+libxml2+lzma~nis~optimizations+pic+pyexpat+pythoncmd+readline+shared+sqlite3+ssl~tix~tkinter~ucs4+uuid+zlib patches=0d98e93189bc278fbc37a50ed7f183bd8aaf249a8e1670a465f0db6bb4f8cf87 arch=linux-centos7-sandybridge^ex...@2.2.10%g...@8.3.0+libbsd arch=linux-centos7-sandybridge^lib...@0.10.0%g...@8.3.0 arch=linux-centos7-sandybridge^get...@0.21%g...@8.3.0+bzip2+curses+git~libunistring+libxml2+tar+xz arch=linux-centos7-sandybridge^t...@1.32%g...@8.3.0 arch=linux-centos7-sandybridge^libffi@3.3%g...@8.3.0 patches=26f26c6f29a7ce9bf370ad3ab2610f99365b4bdd7b82e7c31df41a3370d685c0 arch=linux-centos7-sandybridge^lib...@1.0.3%g...@8.3.0 arch=linux-centos7-sandybridge
^sql...@3.33.0%g...@8.3.0+column_metadata+fts~functions~rtree arch=linux-centos7-sandybridge
Of course, as usual, I do not understand the meaning of these words, or what is the next step...Thanks a lot.