error during installation with spack on CentOS7

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Alberto Salvadori

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Oct 1, 2019, 1:02:43 PM10/1/19
to deal.II User Group
Dear community

I have been trying to install deal.ii on a linux machine equipped with CentOS7. As very clearly explained in " https://github.com/dealii/dealii/wiki/deal.II-in-Spack#check-before-build "
I have installed the latest version of gcc, openmpi, cmake.

[deal.ii@localhost spack]$ gcc --version

gcc (GCC) 9.2.0

Copyright (C) 2019 Free Software Foundation, Inc.

This is free software; see the source for copying conditions.  There is NO

warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.


[deal.ii@localhost spack]$ mpirun --version

mpirun (Open MPI) 3.1.4


[deal.ii@localhost spack]$ cmake --version

cmake version 3.15.3


Noticing the incompatibility with cmake, I run

[deal.ii@localhost spack]$ spack install dealii^cm...@3.9.4




but I got this error:



==> libsigsegv is already installed in /home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/libsigsegv-2.11-brkulrpubdu66nzym2zt2j6c3h6nw463

==> m4 is already installed in /home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/m4-1.4.18-23npyrcdfzqehgp4s2mhka4nknjjkbzt

==> pkgconf is already installed in /home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/pkgconf-1.6.1-qtpkfoaa5ae54s4icmqie5hbtz6murqx

==> ncurses is already installed in /home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/ncurses-6.1-awd5putjsuzsddipc35vxiupdjicseao

==> readline is already installed in /home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/readline-7.0-tftx53fdsvjjtfzsfadhzrplo7w2yf46

==> gdbm is already installed in /home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/gdbm-1.18.1-chqdjuttuqyeyrmsnm6yistdpigsguwq

==> Installing perl

==> Searching for binary cache of perl

==> Warning: No Spack mirrors are currently configured

==> No binary for perl found: installing from source

==> Using cached archive: /home/deal.ii/spack/var/spack/cache/perl/perl-5.26.2.tar.gz

==> Using cached archive: /home/deal.ii/spack/var/spack/cache/perl/cpanm-5.26.2.tar.gz

==> Using cached archive: /home/deal.ii/spack/var/spack/cache/perl/perl-5.26.1-guard_old_libcrypt_fix.patch

==> Staging archive: /tmp/deal.ii/spack-stage/perl-5.26.2-zoihbi4ixpd7iyaf5qrbvld62itpgde3/perl-5.26.2.tar.gz

==> Created stage in /tmp/deal.ii/spack-stage/perl-5.26.2-zoihbi4ixpd7iyaf5qrbvld62itpgde3

==> Staging archive: /tmp/deal.ii/spack-stage/resource-cpanm-zoihbi4ixpd7iyaf5qrbvld62itpgde3/App-cpanminus-1.7042.tar.gz

==> Created stage in /tmp/deal.ii/spack-stage/resource-cpanm-zoihbi4ixpd7iyaf5qrbvld62itpgde3

==> Moving resource stage

source : /tmp/deal.ii/spack-stage/resource-cpanm-zoihbi4ixpd7iyaf5qrbvld62itpgde3/spack-src/

destination : /tmp/deal.ii/spack-stage/perl-5.26.2-zoihbi4ixpd7iyaf5qrbvld62itpgde3/spack-src/cpanm/cpanm

==> Applied patch https://src.fedoraproject.org/rpms/perl/raw/004cea3a67df42e92ffdf4e9ac36d47a3c6a05a4/f/perl-5.26.1-guard_old_libcrypt_fix.patch

==> Building perl [Package]

==> Executing phase: 'configure'

==> Executing phase: 'build'

==> Error: ProcessError: Command exited with status 2:

    'make' '-j12'


17 errors found in build log:

     5085    LD_LIBRARY_PATH=/tmp/deal.ii/spack-stage/perl-5.26.2-zoihbi4ixpd7iyaf5qrbvld62itpgde3/spack-src ./miniperl -Ilib make_ext.pl lib/auto/PerlIO/encoding/encoding.so  MAKE="make" LIBPERL_A=libperl.so LINKTYPE=dynamic

     5086    mv Base64.xsc Base64.c

     5087    cc -c   -D_REENTRANT -D_GNU_SOURCE -DAPPLLIB_EXP="/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/perl-5.26.2-zoihbi4ixpd7iyaf5qrbvld62itpgde3/lib/perl5" -fwrapv -fno-strict-aliasing -pipe -fstack-protector-strong -I/home/

             deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/gdbm-1.18.1-chqdjuttuqyeyrmsnm6yistdpigsguwq/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -Wall -Werror=declaration-after-statement -Wextra -Wc++-compat -Wwrite-strings -O2  

              -DVERSION=\"3.15\" -DXS_VERSION=\"3.15\" -fPIC "-I../.."   Base64.c

     5088    In file included from ../../perl.h:5644,

     5089                     from IO.xs:12:

     5090    IO.xs: In function 'XS_IO__Poll__poll':

  >> 5091    IO.xs:321:51: error: invalid application of 'sizeof' to incomplete type 'struct pollfd'

     5092      321 |     SV *tmpsv = sv_2mortal(NEWSV(999,nfd * sizeof(struct pollfd)));

     5093          |                                                   ^~~~~~

     5094    ../../embed.h:596:46: note: in definition of macro 'sv_2mortal'

     5095      596 | #define sv_2mortal(a)  Perl_sv_2mortal(aTHX_ a)

     5096          |                                              ^

     5097    ../../handy.h:2258:22: note: in expansion of macro 'newSV'

     5098     2258 | #define NEWSV(x,len) newSV(len)

     5099          |                      ^~~~~

     5100    IO.xs:321:28: note: in expansion of macro 'NEWSV'

     5101      321 |     SV *tmpsv = sv_2mortal(NEWSV(999,nfd * sizeof(struct pollfd)));

     5102          |                            ^~~~~

     5103    mv NDBM_File.xsc NDBM_File.c

  >> 5104    IO.xs:328:5: error: invalid use of undefined type 'struct pollfd'

     5105      328 |  fds[j].fd = SvIV(ST(i));

     5106          |     ^

  >> 5107    IO.xs:328:5: error: dereferencing pointer to incomplete type 'struct pollfd'

  >> 5108    IO.xs:330:5: error: invalid use of undefined type 'struct pollfd'

     5109      330 |  fds[j].events = (short)SvIV(ST(i));

     5110          |     ^

  >> 5111    IO.xs:332:5: error: invalid use of undefined type 'struct pollfd'

     5112      332 |  fds[j].revents = 0;

     5113          |     ^

     5114    /tmp/deal.ii/spack-stage/perl-5.26.2-zoihbi4ixpd7iyaf5qrbvld62itpgde3/spack-src/ext/NDBM_File/../../miniperl "-I../../lib" -MExtUtils::Command::MM -e 'cp_nonempty' -- NDBM_File.bs ../../lib/auto/NDBM_File/NDBM_File.bs 644

     5115    IO.xs:334:15: warning: implicit declaration of function 'poll'; did you mean 'powl'? [-Wimplicit-function-declaration]

     5116      334 |     if((ret = poll(fds,nfd,timeout)) >= 0) {

     5117          |               ^~~~

     5118          |               powl

     5119    In file included from ../../perl.h:5644,

     5120                     from IO.xs:12:

  >> 5121    IO.xs:336:25: error: invalid use of undefined type 'struct pollfd'

     5122      336 |      sv_setiv(ST(i), fds[j].fd); i++;

     5123          |                         ^

     5124    ../../embed.h:674:46: note: in definition of macro 'sv_setiv'

     5125      674 | #define sv_setiv(a,b)  Perl_sv_setiv(aTHX_ a,b)

     5126          |                                              ^

  >> 5127    IO.xs:337:25: error: invalid use of undefined type 'struct pollfd'

     5128      337 |      sv_setiv(ST(i), fds[j].revents); i++;

     5129          |                         ^

     5130    ../../embed.h:674:46: note: in definition of macro 'sv_setiv'

     5131      674 | #define sv_setiv(a,b)  Perl_sv_setiv(aTHX_ a,b)

     5132          |                                              ^

     5133    Running Mkbootstrap for Opcode ()

     5134    cc -c   -D_REENTRANT -D_GNU_SOURCE -DAPPLLIB_EXP="/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/perl-5.26.2-zoihbi4ixpd7iyaf5qrbvld62itpgde3/lib/perl5" -fwrapv -fno-strict-aliasing -pipe -fstack-protector-strong -I/home/

             deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/gdbm-1.18.1-chqdjuttuqyeyrmsnm6yistdpigsguwq/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -Wall -Werror=declaration-after-statement -Wextra -Wc++-compat -Wwrite-strings -O2  

              -DVERSION=\"1.14\" -DXS_VERSION=\"1.14\" -fPIC "-I../.."   NDBM_File.c

     5135    mv ListUtil.xsc ListUtil.c

     5136    chmod 755 ../../../lib/auto/Encode/CN/CN.so

     5137    /tmp/deal.ii/spack-stage/perl-5.26.2-zoihbi4ixpd7iyaf5qrbvld62itpgde3/spack-src/cpan/Scalar-List-Utils/../../miniperl "-I../../lib" -MExtUtils::Command::MM -e 'cp_nonempty' -- Util.bs ../../lib/auto/List/Util/Util.bs 644

     5138    make[2]: Leaving directory `/tmp/deal.ii/spack-stage/perl-5.26.2-zoihbi4ixpd7iyaf5qrbvld62itpgde3/spack-src/cpan/Encode/CN'

  >> 5139    make[1]: *** [IO.o] Error 1

     5140    make[1]: Leaving directory `/tmp/deal.ii/spack-stage/perl-5.26.2-zoihbi4ixpd7iyaf5qrbvld62itpgde3/spack-src/dist/IO'

     5141    chmod 644 "Opcode.bs"

     5142    "../../miniperl" "-I../../lib" "../../lib/ExtUtils/xsubpp"  -typemap '/tmp/deal.ii/spack-stage/perl-5.26.2-zoihbi4ixpd7iyaf5qrbvld62itpgde3/spack-src/ext/Opcode/../../lib/ExtUtils/typemap'  Opcode.xs > Opcode.xsc

     5143    make[1]: Entering directory `/tmp/deal.ii/spack-stage/perl-5.26.2-zoihbi4ixpd7iyaf5qrbvld62itpgde3/spack-src/dist/IO'

     5144    make[2]: Entering directory `/tmp/deal.ii/spack-stage/perl-5.26.2-zoihbi4ixpd7iyaf5qrbvld62itpgde3/spack-src/cpan/Encode/EBCDIC'

     5145    cc -c   -D_REENTRANT -D_GNU_SOURCE -DAPPLLIB_EXP="/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/perl-5.26.2-zoihbi4ixpd7iyaf5qrbvld62itpgde3/lib/perl5" -fwrapv -fno-strict-aliasing -pipe -fstack-protector-strong -I/home/

             deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/gdbm-1.18.1-chqdjuttuqyeyrmsnm6yistdpigsguwq/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -Wall -Werror=declaration-after-statement -Wextra -Wc++-compat -Wwrite-strings -O2  

              -DVERSION=\"1.46_02\" -DXS_VERSION=\"1.46_02\" -fPIC "-I../.."  -DPERL_EXT ListUtil.c


     ...


     5170    Reading posix-bc (posix-bc)

     5171    /tmp/deal.ii/spack-stage/perl-5.26.2-zoihbi4ixpd7iyaf5qrbvld62itpgde3/spack-src/cpan/Encode/EBCDIC/../../../miniperl "-I../../../lib" -MExtUtils::Command::MM -e 'cp_nonempty' -- EBCDIC.bs ../../../lib/auto/Encode/EBCDIC/EBCDIC.bs 644

     5172    "../../../miniperl" "-I../../../lib" "../../../lib/ExtUtils/xsubpp"  -nolinenumbers -typemap '/tmp/deal.ii/spack-stage/perl-5.26.2-zoihbi4ixpd7iyaf5qrbvld62itpgde3/spack-src/cpan/Encode/EBCDIC/../../../lib/ExtUtils/typemap'  EBCDIC.xs > E

             BCDIC.xsc

     5173    In file included from ../../perl.h:5644,

     5174                     from IO.xs:12:

     5175    IO.xs: In function 'XS_IO__Poll__poll':

  >> 5176    IO.xs:321:51: error: invalid application of 'sizeof' to incomplete type 'struct pollfd'

     5177      321 |     SV *tmpsv = sv_2mortal(NEWSV(999,nfd * sizeof(struct pollfd)));

     5178          |                                                   ^~~~~~

     5179    ../../embed.h:596:46: note: in definition of macro 'sv_2mortal'

     5180      596 | #define sv_2mortal(a)  Perl_sv_2mortal(aTHX_ a)

     5181          |                                              ^

     5182    ../../handy.h:2258:22: note: in expansion of macro 'newSV'

     5183     2258 | #define NEWSV(x,len) newSV(len)

     5184          |                      ^~~~~

     5185    IO.xs:321:28: note: in expansion of macro 'NEWSV'

     5186      321 |     SV *tmpsv = sv_2mortal(NEWSV(999,nfd * sizeof(struct pollfd)));

     5187          |                            ^~~~~

  >> 5188    IO.xs:328:5: error: invalid use of undefined type 'struct pollfd'

     5189      328 |  fds[j].fd = SvIV(ST(i));

     5190          |     ^

  >> 5191    IO.xs:328:5: error: dereferencing pointer to incomplete type 'struct pollfd'

  >> 5192    IO.xs:330:5: error: invalid use of undefined type 'struct pollfd'

     5193      330 |  fds[j].events = (short)SvIV(ST(i));

     5194          |     ^

  >> 5195    IO.xs:332:5: error: invalid use of undefined type 'struct pollfd'

     5196      332 |  fds[j].revents = 0;

     5197          |     ^

     5198    IO.xs:334:15: warning: implicit declaration of function 'poll'; did you mean 'powl'? [-Wimplicit-function-declaration]

     5199      334 |     if((ret = poll(fds,nfd,timeout)) >= 0) {

     5200          |               ^~~~

     5201          |               powl

     5202    In file included from ../../perl.h:5644,

     5203                     from IO.xs:12:

  >> 5204    IO.xs:336:25: error: invalid use of undefined type 'struct pollfd'

     5205      336 |      sv_setiv(ST(i), fds[j].fd); i++;

     5206          |                         ^

     5207    ../../embed.h:674:46: note: in definition of macro 'sv_setiv'

     5208      674 | #define sv_setiv(a,b)  Perl_sv_setiv(aTHX_ a,b)

     5209          |                                              ^

  >> 5210    IO.xs:337:25: error: invalid use of undefined type 'struct pollfd'

     5211      337 |      sv_setiv(ST(i), fds[j].revents); i++;

     5212          |                         ^

     5213    ../../embed.h:674:46: note: in definition of macro 'sv_setiv'

     5214      674 | #define sv_setiv(a,b)  Perl_sv_setiv(aTHX_ a,b)

     5215          |                                              ^

     5216    In file included from ODBM_File.xs:12:

     5217    /home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/gdbm-1.18.1-chqdjuttuqyeyrmsnm6yistdpigsguwq/include/dbm.h:35:12: warning: identifier 'delete' conflicts with C++ keyword [-Wc++-compat]

     5218       35 | extern int delete (datum key);

     5219          |            ^~~~~~

  >> 5220    make[1]: *** [IO.o] Error 1

     5221    make[1]: Leaving directory `/tmp/deal.ii/spack-stage/perl-5.26.2-zoihbi4ixpd7iyaf5qrbvld62itpgde3/spack-src/dist/IO'

     5222    Unsuccessful make(dist/IO): code=512 at make_ext.pl line 570.

  >> 5223    make: *** [lib/auto/IO/IO.so] Error 25

     5224    make: *** Waiting for unfinished jobs....

     5225    cc -c -I./Encode  -I../Encode -D_REENTRANT -D_GNU_SOURCE -DAPPLLIB_EXP="/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/perl-5.26.2-zoihbi4ixpd7iyaf5qrbvld62itpgde3/lib/perl5" -fwrapv -fno-strict-aliasing -pipe -fstack-pro

             tector-strong -I/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/gdbm-1.18.1-chqdjuttuqyeyrmsnm6yistdpigsguwq/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -Wall -Werror=declaration-after-statement -Wextra -Wc++-compat

              -Wwrite-strings -O2   -DVERSION=\"2.02\" -DXS_VERSION=\"2.02\" -fPIC "-I../../.."   ebcdic_t.c

     5226    ODBM_File.c: In function 'XS_ODBM_File_STORE':

     5227    ODBM_File.c:406:6: warning: variable 'flags' set but not used [-Wunused-but-set-variable]

     5228      406 |  int flags;

     5229          |      ^~~~~


See build log for details:

  /tmp/deal.ii/spack-stage/perl-5.26.2-zoihbi4ixpd7iyaf5qrbvld62itpgde3/spack-build-out.txt


Can you perhaps provide suggestions on what possibly went wrong? To add further information, I did not add any limit version of suite-sparse, i.e.

[deal.ii@localhost spack]$ more ~/.spack/linux/packages.yaml

packages:

  all:

    compiler: [gcc]

    providers:

      mpi: [openmpi]

  openmpi:

    version: [3.1.4]

    paths:

      ope...@3.1.4%g...@9.2.0: /usr/local/

    buildable: False

  dealii:

    variants: +optflags~python


[deal.ii@localhost spack]$ more ~/.spack/linux/compilers.yaml 

compilers:

- compiler:

    environment: {}

    extra_rpaths: []

    flags: {}

    modules: []

    operating_system: centos7

    paths:

      cc: /usr/bin/gcc

      cxx: /usr/bin/g++

      f77: /usr/bin/gfortran

      fc: /usr/bin/gfortran

    spec: g...@4.8.5

    target: x86_64

- compiler:

    environment: {}

    extra_rpaths: []

    flags: {}

    modules: []

    operating_system: centos7

    paths:

      cc: /usr/local/bin/gcc

      cxx: /usr/local/bin/g++

      f77: /usr/local/bin/gfortran

      fc: /usr/local/bin/gfortran

    spec: g...@9.2.0

    target: x86_64


I take advantage to ask further help with lapack. I do see a lapack library installed, 

[deal.ii@localhost spack]$ ls -lta /usr/lib64/liblapacke*.*

lrwxrwxrwx. 1 root root      19 18 ott  2018 /usr/lib64/liblapacke.so.3 -> liblapacke.so.3.4.2

lrwxrwxrwx. 1 root root      19 18 ott  2018 /usr/lib64/liblapacke.so.3.4 -> liblapacke.so.3.4.2

-rwxr-xr-x. 1 root root 1965960  2 ago  2017 /usr/lib64/liblapacke.so.3.4.2


but I cannot see any blas. What would you recommend me to set in the System provided packages ? I appreciate your help as always

Alberto









Wolfgang Bangerth

unread,
Oct 1, 2019, 4:51:19 PM10/1/19
to dea...@googlegroups.com
On 10/1/19 11:02 AM, Alberto Salvadori wrote:
>
> Can you perhaps provide suggestions on what possibly went wrong? To add
> further information, I did not add any limit version of suite-sparse, i.e.

It looks to me like spack fails while compiling Perl. I don't think there's
anything we can do about it from our side -- please report this to the spack
forums.

In your last question, are you asking what the correct package is to install
BLAS on your system? I would strongly suspect that if you have lapack
installed, then blas must be installed somewhere as well. You might be able to
find out where by doing
ldd /usr/lib64/liblapacke.so.3.4.2

Best
W.

--
------------------------------------------------------------------------
Wolfgang Bangerth email: bang...@colostate.edu
www: http://www.math.colostate.edu/~bangerth/

Denis Davydov

unread,
Oct 2, 2019, 12:26:01 AM10/2/19
to deal.II User Group
Hi Alberto,

Such issues should ideally be reported to Perl, because that's the issue with their package. Or at least to Spack in a hope that the community can come up with some patch to workaround the build issue in Perl.

For you to go on simply tell Spack to use Perl from system:

perl:
        paths:
             pe...@5.26.2%g...@9.2.0: /usr

As for the Blas/Lapack, IMO there is no reason to use system provided one in your case. 
You get more control of threading, compiler flags, etc through Spack and it does not take ages to build either.

p.s. there are some examples of config files for Spack on various HPC systems, if that helps:



Denis.

Alberto Salvadori

unread,
Oct 2, 2019, 7:20:06 AM10/2/19
to dea...@googlegroups.com
Thank you so much W and D,
As you pointed out there seems to be a mistake in the most recent version of perl during installation.
I will point this out in the proper communities. 

As Denis proposed 





Alberto Salvadori
 Dipartimento di Ingegneria Meccanica e Industriale (DIMI)
 Universita` di Brescia, via Branze 43, 25123 Brescia
 Italy
 tel 030 3711239
 fax 030 3711312

e-mail:
 alberto....@unibs.it
web-page:
 http://m4lab.unibs.it/faculty.html



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Informativa sulla Privacy: http://www.unibs.it/node/8155

Alberto Salvadori

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Oct 2, 2019, 7:24:32 AM10/2/19
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Thank you so much W and D,
As you pointed out there seems to be a mistake in the most recent version of perl during installation.
I will propagate this to the proper communities. 

As Denis proposed, I went on simply tell Spack to use Perl from system:

perl:
        paths:
             pe...@5.26.2%g...@9.2.0: /usr

but I bumped into another issue:

[deal.ii@localhost spack]$ spack install dealii^cm...@3.9.4

==> libsigsegv is already installed in /home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/libsigsegv-2.11-brkulrpubdu66nzym2zt2j6c3h6nw463

==> m4 is already installed in /home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/m4-1.4.18-23npyrcdfzqehgp4s2mhka4nknjjkbzt

==> pe...@5.16.3 : externally installed in /usr

==> pe...@5.16.3 : already registered in DB

==> autoconf is already installed in /home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/autoconf-2.69-2vk2foufmuyjm2gh47u6nouxezza3p6p

==> automake is already installed in /home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/automake-1.16.1-z52jybnv7ass3otkgegjazvdbbughw2q

==> libtool is already installed in /home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/libtool-2.4.6-mr3m4npcnryydzctugoebk2zuoav7zte

==> adol-c is already installed in /home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/adol-c-develop-xioth2pegguh6rb6mzfzk7zhvb2kgeue

==> pkgconf is already installed in /home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/pkgconf-1.6.1-qtpkfoaa5ae54s4icmqie5hbtz6murqx

==> ncurses is already installed in /home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/ncurses-6.1-awd5putjsuzsddipc35vxiupdjicseao

==> zlib is already installed in /home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/zlib-1.2.11-fa7l75havytsbgz77sh6yyzvqgmmm5dj

==> openssl is already installed in /home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/openssl-1.1.1c-ou63dp5nv43t2vudcv44rc753i7yecl2

==> Installing cmake

==> Searching for binary cache of cmake

==> Warning: No Spack mirrors are currently configured

==> No binary for cmake found: installing from source

==> Using cached archive: /home/deal.ii/spack/var/spack/cache/cmake/cmake-3.9.4.tar.gz

==> Staging archive: /tmp/deal.ii/spack-stage/cmake-3.9.4-jy2ih5ctlebz57xqk7kvgzv22tabfbq4/cmake-3.9.4.tar.gz

==> Created stage in /tmp/deal.ii/spack-stage/cmake-3.9.4-jy2ih5ctlebz57xqk7kvgzv22tabfbq4

==> Applied patch /home/deal.ii/spack/var/spack/repos/builtin/packages/cmake/nag-response-files.patch

==> Building cmake [Package]

==> Executing phase: 'bootstrap'

==> Error: ProcessError: Command exited with status 11:

    './bootstrap' '--prefix=/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/cmake-3.9.4-jy2ih5ctlebz57xqk7kvgzv22tabfbq4' '--parallel=12' '--no-system-libs' '--no-qt-gui' '--' '-DCMAKE_USE_OPENSSL=True'


1 error found in build log:

     196    /home/deal.ii/spack/lib/spack/env/gcc/g++   -std=gnu++14     -I/tmp/deal.ii/spack-stage/cmake-3.9.4-jy2ih5ctlebz57xqk7kvgzv22tabfbq4/spack-src/Bootstrap.cmk   -I/tmp/deal.ii/spack-stage/cmake-3.9.4-jy2ih5ctlebz57xqk7kvgzv22tabfbq4/spack-sr

            c/Source   -I/tmp/deal.ii/spack-stage/cmake-3.9.4-jy2ih5ctlebz57xqk7kvgzv22tabfbq4/spack-src/Source/LexerParser   -I/tmp/deal.ii/spack-stage/cmake-3.9.4-jy2ih5ctlebz57xqk7kvgzv22tabfbq4/spack-src/Utilities  cmAddCustomCommandCommand.o cmAd

            dCustomTargetCommand.o cmAddDefinitionsCommand.o cmAddDependenciesCommand.o cmAddExecutableCommand.o cmAddLibraryCommand.o cmAddSubDirectoryCommand.o cmAddTestCommand.o cmBreakCommand.o cmBuildCommand.o cmCMakeMinimumRequired.o cmCMakePoli

            cyCommand.o cmCPackPropertiesGenerator.o cmCacheManager.o cmCommand.o cmCommandArgumentParserHelper.o cmCommandArgumentsHelper.o cmCommands.o cmCommonTargetGenerator.o cmComputeComponentGraph.o cmComputeLinkDepends.o cmComputeLinkInformati

            on.o cmComputeTargetDepends.o cmConditionEvaluator.o cmConfigureFileCommand.o cmContinueCommand.o cmCoreTryCompile.o cmCreateTestSourceList.o cmCustomCommand.o cmCustomCommandGenerator.o cmDefinePropertyCommand.o cmDefinitions.o cmDepends.

            o cmDependsC.o cmDisallowedCommand.o cmDocumentationFormatter.o cmEnableLanguageCommand.o cmEnableTestingCommand.o cmExecProgramCommand.o cmExecuteProcessCommand.o cmExpandedCommandArgument.o cmExportBuildFileGenerator.o cmExportFileGenera

            tor.o cmExportInstallFileGenerator.o cmExportSet.o cmExportSetMap.o cmExportTryCompileFileGenerator.o cmExprParserHelper.o cmExternalMakefileProjectGenerator.o cmFileCommand.o cmFileTimeComparison.o cmFindBase.o cmFindCommon.o cmFindFileCo

            mmand.o cmFindLibraryCommand.o cmFindPackageCommand.o cmFindPathCommand.o cmFindProgramCommand.o cmForEachCommand.o cmFunctionCommand.o cmGeneratedFileStream.o cmGeneratorExpression.o cmGeneratorExpressionContext.o cmGeneratorExpressionDAG

            Checker.o cmGeneratorExpressionEvaluationFile.o cmGeneratorExpressionEvaluator.o cmGeneratorExpressionLexer.o cmGeneratorExpressionNode.o cmGeneratorExpressionParser.o cmGeneratorTarget.o cmGetCMakePropertyCommand.o cmGetDirectoryPropertyC

            ommand.o cmGetFilenameComponentCommand.o cmGetPropertyCommand.o cmGetSourceFilePropertyCommand.o cmGetTargetPropertyCommand.o cmGetTestPropertyCommand.o cmGlobalCommonGenerator.o cmGlobalGenerator.o cmGlobalUnixMakefileGenerator3.o cmHexFi

            leConverter.o cmIfCommand.o cmIncludeCommand.o cmIncludeDirectoryCommand.o cmIncludeRegularExpressionCommand.o cmInstallCommand.o cmInstallCommandArguments.o cmInstallDirectoryGenerator.o cmInstallExportGenerator.o cmInstallFilesCommand.o 

            cmInstallFilesGenerator.o cmInstallGenerator.o cmInstallScriptGenerator.o cmInstallTargetGenerator.o cmInstallTargetsCommand.o cmInstalledFile.o cmLinkDirectoriesCommand.o cmLinkLineComputer.o cmListCommand.o cmListFileCache.o cmLocalCommo

            nGenerator.o cmLocalGenerator.o cmLocalUnixMakefileGenerator3.o cmMSVC60LinkLineComputer.o cmMacroCommand.o cmMakeDirectoryCommand.o cmMakefile.o cmMakefileExecutableTargetGenerator.o cmMakefileLibraryTargetGenerator.o cmMakefileTargetGene

            rator.o cmMakefileUtilityTargetGenerator.o cmMarkAsAdvancedCommand.o cmMathCommand.o cmMessageCommand.o cmMessenger.o cmNewLineStyle.o cmOSXBundleGenerator.o cmOptionCommand.o cmOrderDirectories.o cmOutputConverter.o cmParseArgumentsComman

            d.o cmPathLabel.o cmPolicies.o cmProcessOutput.o cmProjectCommand.o cmProperty.o cmPropertyDefinition.o cmPropertyDefinitionMap.o cmPropertyMap.o cmReturnCommand.o cmRulePlaceholderExpander.o cmScriptGenerator.o cmSearchPath.o cmSeparateAr

            gumentsCommand.o cmSetCommand.o cmSetDirectoryPropertiesCommand.o cmSetPropertyCommand.o cmSetSourceFilesPropertiesCommand.o cmSetTargetPropertiesCommand.o cmSetTestsPropertiesCommand.o cmSiteNameCommand.o cmSourceFile.o cmSourceFileLocati

            on.o cmState.o cmStateDirectory.o cmStateSnapshot.o cmStringCommand.o cmSubdirCommand.o cmSystemTools.o cmTarget.o cmTargetLinkLibrariesCommand.o cmTargetPropertyComputer.o cmTest.o cmTestGenerator.o cmTimestamp.o cmTryCompileCommand.o cmT

            ryRunCommand.o cmUnexpectedCommand.o cmUnsetCommand.o cmVersion.o cmWhileCommand.o cmWorkingDirectory.o cmake.o cmakemain.o cmcmd.o cmCommandArgumentLexer.o cmCommandArgumentParser.o cmExprLexer.o cmExprParser.o cmListFileLexer.o Directory

            .o EncodingCXX.o FStream.o Glob.o RegularExpression.o SystemTools.o EncodingC.o ProcessUNIX.o String.o System.o Terminal.o -o cmake

     197    /tmp/deal.ii/spack-stage/cmake-3.9.4-jy2ih5ctlebz57xqk7kvgzv22tabfbq4/spack-src/Bootstrap.cmk/cmake: /lib64/libstdc++.so.6: version `GLIBCXX_3.4.26' not found (required by /tmp/deal.ii/spack-stage/cmake-3.9.4-jy2ih5ctlebz57xqk7kvgzv22tabfb

            q4/spack-src/Bootstrap.cmk/cmake)

     198    /tmp/deal.ii/spack-stage/cmake-3.9.4-jy2ih5ctlebz57xqk7kvgzv22tabfbq4/spack-src/Bootstrap.cmk/cmake: /lib64/libstdc++.so.6: version `CXXABI_1.3.9' not found (required by /tmp/deal.ii/spack-stage/cmake-3.9.4-jy2ih5ctlebz57xqk7kvgzv22tabfbq4

            /spack-src/Bootstrap.cmk/cmake)

     199    /tmp/deal.ii/spack-stage/cmake-3.9.4-jy2ih5ctlebz57xqk7kvgzv22tabfbq4/spack-src/Bootstrap.cmk/cmake: /lib64/libstdc++.so.6: version `GLIBCXX_3.4.20' not found (required by /tmp/deal.ii/spack-stage/cmake-3.9.4-jy2ih5ctlebz57xqk7kvgzv22tabfb

            q4/spack-src/Bootstrap.cmk/cmake)

     200    /tmp/deal.ii/spack-stage/cmake-3.9.4-jy2ih5ctlebz57xqk7kvgzv22tabfbq4/spack-src/Bootstrap.cmk/cmake: /lib64/libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by /tmp/deal.ii/spack-stage/cmake-3.9.4-jy2ih5ctlebz57xqk7kvgzv22tabfb

            q4/spack-src/Bootstrap.cmk/cmake)

     201    ---------------------------------------------

  >> 202    Error when bootstrapping CMake:

     203    Problem while running initial CMake

     204    ---------------------------------------------


See build log for details:

  /tmp/deal.ii/spack-stage/cmake-3.9.4-jy2ih5ctlebz57xqk7kvgzv22tabfbq4/spack-build-out.txt




Is it perhaps due to a conflict between cmake and the gcc compiler versions? Can you perhaps address me how to sort this out?

I appreciate,
Alberto


Alberto Salvadori
 Dipartimento di Ingegneria Meccanica e Industriale (DIMI)
 Universita` di Brescia, via Branze 43, 25123 Brescia
 Italy
 tel 030 3711239
 fax 030 3711312

e-mail:
 alberto....@unibs.it
web-page:
 http://m4lab.unibs.it/faculty.html

Bruno Turcksin

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Oct 2, 2019, 8:41:47 AM10/2/19
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Alberto,


On Wednesday, October 2, 2019 at 7:24:32 AM UTC-4, Alberto Salvadori wrote:
Thank you so much W and D,
As you pointed out there seems to be a mistake in the most recent version of perl during installation.
It looks to me that spack is trying to compile cmake with gcc 9.2 but somehow it is using the libstdc++ library from your system. You can try to load gcc 9.2 or you could just tell spack to use your system compiler.

Best,

Bruno
 

Alberto Salvadori

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Oct 2, 2019, 8:51:17 AM10/2/19
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Thank you, Bruno. In fact, my aim was to use my system compiler. 
Here is my  .spack/linux/packages.yaml:

packages:

  all:

    compiler: [gcc]

    providers:

      mpi: [openmpi]

  openmpi:

    version: [3.1.4]

    paths:

      ope...@3.1.4%g...@9.2.0: /usr/local/

    buildable: False

  perl:

    paths:

      pe...@5.16.3%g...@9.2.0: /usr

  cmake:

    version: [3.15.3]

    paths:

      cm...@3.15.3%g...@9.2.0: /usr/local/

  hdf5:

    version: [1.8.12]

    paths:

      hd...@1.8.12%g...@9.2.0: /usr

    variants: +hl+fortran

  netcdf:

    version: [7.2.0]

    paths:

     net...@7.2.0%g...@9.2.0: /usr 

  netcdf-cxx:

    version: [4.2.8]

    paths:

     netcd...@4.2.8%g...@9.2.0: /usr

  dealii:

    variants: +optflags~python


Shall I perhaps add something to the compiler flag (paths or so)?
Here is also my  .spack/linux/compilers.yaml 
Alberto


Alberto Salvadori
 Dipartimento di Ingegneria Meccanica e Industriale (DIMI)
 Universita` di Brescia, via Branze 43, 25123 Brescia
 Italy
 tel 030 3711239
 fax 030 3711312

e-mail:
 alberto....@unibs.it
web-page:
 http://m4lab.unibs.it/faculty.html

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Alberto Salvadori

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Oct 2, 2019, 9:13:42 AM10/2/19
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Bruno, I guess the point is that cmake invokes  /lib64/libstdc++.so.6 
rather than /usr/local/lib64/libstdc++.so.6 
Is it correct?

Alberto Salvadori
 Dipartimento di Ingegneria Meccanica e Industriale (DIMI)
 Universita` di Brescia, via Branze 43, 25123 Brescia
 Italy
 tel 030 3711239
 fax 030 3711312

e-mail:
 alberto....@unibs.it
web-page:
 http://m4lab.unibs.it/faculty.html

Bruno Turcksin

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Oct 2, 2019, 9:14:46 AM10/2/19
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Alberto,

So what happens is that spack is using gcc 9.2 like you want but it
usess the libstdc++ from gcc 4.8.5 I usually spack to install a new
compiler and my compilers.yaml looks like your *but* I have the path
to the correct libstdc++ in my LD_LIBRARY_PATH when I load the module.
So I guess you need to add that path somewhere in your compilers.yaml

Best,

Bruno

Le mer. 2 oct. 2019 à 08:51, Alberto Salvadori
<alberto....@unibs.it> a écrit :
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Denis Davydov

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Oct 2, 2019, 1:26:06 PM10/2/19
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Hi Alberto,

Looks like the issue is known to Spack community: https://github.com/spack/spack/issues/11224 where there is also a possible source of the problem you can try as a fix (un-do on-line PR).

Regards,
Denis.
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>
>
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Alberto Salvadori

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Oct 4, 2019, 6:38:20 AM10/4/19
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Hi Denis

thanks for your note. I figured out that by adding the path in the compilers.yaml file, in this way

- compiler:

    environment: 

      append-path:

        LD_LIBRARY_PATH: /usr/local/lib64

    extra_rpaths: []

    flags: {}

    modules: []

    operating_system: centos7

    paths:

      cc: /usr/local/bin/gcc

      cxx: /usr/local/bin/g++

      f77: /usr/local/bin/gfortran

      fc: /usr/local/bin/gfortran

    spec: g...@9.2.0

    target: x86_64


sorts out the issue.

Denis Davydov

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Oct 4, 2019, 6:40:28 AM10/4/19
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Great, happy to hear you sorted this out by tweaking compilers.yaml settings.

Alberto Salvadori

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Oct 4, 2019, 6:50:24 AM10/4/19
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Dear community

I apologize for this too long bothering on  installing deal.ii on a linux machine equipped with CentOS7. I am having quite a large amount of issues, perhaps related to the gcc compiler(?). 
The very last, which I was unable to solve up to now, relates to slepc . I wonder if any of you had a similar problem and in case could address its solution.

Here is the outcome of installation via spack:

==> Installing slepc

==> Searching for binary cache of slepc

==> Warning: No Spack mirrors are currently configured

==> No binary for slepc found: installing from source

==> Fetching http://slepc.upv.es/download/distrib/slepc-3.12.0.tar.gz

######################################################################## 100.0%

==> Staging archive: /tmp/deal.ii/spack-stage/slepc-3.12.0-5md6u45rynyaqtcta4e5dmecqhkp2jkr/slepc-3.12.0.tar.gz

==> Created stage in /tmp/deal.ii/spack-stage/slepc-3.12.0-5md6u45rynyaqtcta4e5dmecqhkp2jkr

==> No patches needed for slepc

==> Building slepc [Package]

==> Executing phase: 'install'

==> Error: ProcessError: Command exited with status 1:

    './configure' '--prefix=/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/slepc-3.12.0-5md6u45rynyaqtcta4e5dmecqhkp2jkr' '--with-arpack-dir=/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/arpack-ng-3.7.0-i5fx7mowpxx7acbasidsfc4r3owcd2vx/lib' '--with-arpack-flags=-lparpack,-larpack'

See build log for details:

  /tmp/deal.ii/spack-stage/slepc-3.12.0-5md6u45rynyaqtcta4e5dmecqhkp2jkr/spack-build-out.txt



and the log (s):

==> Executing phase: 'install'

==> [2019-10-03-20:48:03.194513] './configure' '--prefix=/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/slepc-3.12.0-5md6u45rynyaqtcta4e5dmecqhkp2jkr' '--with-arpack-dir=/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/arpack-ng-3.7.0-i5fx7mowpxx7acbasidsfc4r3owcd2vx/lib' '--with-arpack-flags=-lparpack,-larpack'

Checking environment... done

Checking PETSc installation... 

ERROR: Unable to link with PETSc

ERROR: See "installed-arch-linux2-c-opt/lib/slepc/conf/configure.log" file for details



================================================================================

Starting Configure Run at Thu Oct  3 20:48:03 2019

Configure Options: --prefix=/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/slepc-3.12.0-5md6u45rynyaqtcta4e5dmecqhkp2jkr --with-arpack-dir=/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/arpack-ng-3.7.0-i5fx7mowpxx7acbasidsfc4r3owcd2vx/lib --with-arpack-flags=-lparpack,-larpack

Working directory: /tmp/deal.ii/spack-stage/slepc-3.12.0-5md6u45rynyaqtcta4e5dmecqhkp2jkr/spack-src

Python version:

2.7.16 (default, Oct  3 2019, 20:40:41) 

[GCC 9.2.0]

make: /usr/bin/gmake

PETSc source directory: /home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/petsc-3.12.0-7b3mdm63ap32riorneym2mtcmwjlb63s

PETSc install directory: /home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/petsc-3.12.0-7b3mdm63ap32riorneym2mtcmwjlb63s

PETSc version: 3.12.0

SLEPc source directory: /tmp/deal.ii/spack-stage/slepc-3.12.0-5md6u45rynyaqtcta4e5dmecqhkp2jkr/spack-src

SLEPc install directory: /home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/slepc-3.12.0-5md6u45rynyaqtcta4e5dmecqhkp2jkr

SLEPc version: 3.12.0

================================================================================

Checking PETSc installation...

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 

Running command:

cd /tmp/slepc-7TxU8j;/usr/bin/gmake checklink TESTFLAGS=""

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 

#include "petscsnes.h"

int main() {

Vec v; Mat m; KSP k;

PetscInitializeNoArguments();

VecCreate(PETSC_COMM_WORLD,&v);

MatCreate(PETSC_COMM_WORLD,&m);

KSPCreate(PETSC_COMM_WORLD,&k);

return 0;

}

/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/openmpi-3.1.4-4lzhe2gtz3nzhffn6efu2fzgochphcix/bin/mpicc -o checklink.o -c -fPIC   -I/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/petsc-3.12.0-7b3mdm63ap32riorneym2mtcmwjlb63s/include -I/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/hypre-2.18.0-dbexk2cnwvnsjd5fm6ltw7o7q66ik3hy/include -I/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/superlu-dist-6.1.1-stsykz4xojdqtlnjavms2opkppopzush/include -I/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/hdf5-1.10.5-lt5jyi3ix6dbrbblku7ygutgek7wg5w2/include -I/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/parmetis-4.0.3-p3vaameiqho6enhkpjhcupk5lam6jvc6/include -I/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/metis-5.1.0-zepovp3vvqzcirbxoqyb33fg5mm26spe/include -I/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/zlib-1.2.11-fa7l75havytsbgz77sh6yyzvqgmmm5dj/include    `pwd`/checklink.c

/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/openmpi-3.1.4-4lzhe2gtz3nzhffn6efu2fzgochphcix/bin/mpicc -fPIC  -o checklink checklink.o  -Wl,-rpath,/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/petsc-3.12.0-7b3mdm63ap32riorneym2mtcmwjlb63s/lib -L/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/petsc-3.12.0-7b3mdm63ap32riorneym2mtcmwjlb63s/lib -Wl,-rpath,/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/hypre-2.18.0-dbexk2cnwvnsjd5fm6ltw7o7q66ik3hy/lib -L/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/hypre-2.18.0-dbexk2cnwvnsjd5fm6ltw7o7q66ik3hy/lib -Wl,-rpath,/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/superlu-dist-6.1.1-stsykz4xojdqtlnjavms2opkppopzush/lib -L/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/superlu-dist-6.1.1-stsykz4xojdqtlnjavms2opkppopzush/lib -Wl,-rpath,/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/openblas-0.3.7-2dvho7dpjd4bndibkwb7hocq2jcjri3a/lib -L/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/openblas-0.3.7-2dvho7dpjd4bndibkwb7hocq2jcjri3a/lib -Wl,-rpath,/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/hdf5-1.10.5-lt5jyi3ix6dbrbblku7ygutgek7wg5w2/lib -L/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/hdf5-1.10.5-lt5jyi3ix6dbrbblku7ygutgek7wg5w2/lib -Wl,-rpath,/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/parmetis-4.0.3-p3vaameiqho6enhkpjhcupk5lam6jvc6/lib -L/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/parmetis-4.0.3-p3vaameiqho6enhkpjhcupk5lam6jvc6/lib -Wl,-rpath,/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/metis-5.1.0-zepovp3vvqzcirbxoqyb33fg5mm26spe/lib -L/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/metis-5.1.0-zepovp3vvqzcirbxoqyb33fg5mm26spe/lib -Wl,-rpath,/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/zlib-1.2.11-fa7l75havytsbgz77sh6yyzvqgmmm5dj/lib -L/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/zlib-1.2.11-fa7l75havytsbgz77sh6yyzvqgmmm5dj/lib -Wl,-rpath,/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/hwloc-1.11.11-admmx7jd2wn63yvpnbp4secnkvhpmevu/lib -L/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/hwloc-1.11.11-admmx7jd2wn63yvpnbp4secnkvhpmevu/lib -Wl,-rpath,/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/openmpi-3.1.4-4lzhe2gtz3nzhffn6efu2fzgochphcix/lib -L/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/openmpi-3.1.4-4lzhe2gtz3nzhffn6efu2fzgochphcix/lib -Wl,-rpath,/usr/local/lib/gcc/x86_64-pc-linux-gnu/9.2.0 -L/usr/local/lib/gcc/x86_64-pc-linux-gnu/9.2.0 -Wl,-rpath,/usr/local/lib64 -L/usr/local/lib64 -Wl,-rpath,/usr/local/lib -L/usr/local/lib -lpetsc -lHYPRE -lsuperlu_dist -lopenblas -lhdf5hl_fortran -lhdf5_fortran -lhdf5_hl -lhdf5 -lparmetis -lmetis -lm -lz -lstdc++ -ldl -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath -lpthread -lquadmath -lstdc++ -ldl

/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/petsc-3.12.0-7b3mdm63ap32riorneym2mtcmwjlb63s/lib/libpetsc.so: undefined reference to `hypre_ParCSRMatrixCompleteClone'

collect2: error: ld returned 1 exit status

gmake: *** [checklink] Error 1


ERROR: Unable to link with PETSc


Could it be related to make? It is still the GNU Make 3.82 . Thank you so much
Alberto

Denis Davydov

unread,
Oct 4, 2019, 6:54:23 AM10/4/19
to deal.II User Group
Hi Alberto,

Try reporting issue on Spack Github and ping @balay .

Denis.

Alberto Salvadori

unread,
Oct 7, 2019, 12:10:48 PM10/7/19
to deal.II User Group

For further information, hoping this can be of use,
it turned out that the very same error in slepc installation occurs with g...@7.4.0 .
This strikes me a bit, because I did install deal.ii with such a compiler on a ubuntu machine,  rather than CentOS7, via spack.
The issue was reported on Spack Github.
Thank you,

Alberto

Alberto Salvadori

unread,
Oct 9, 2019, 3:30:18 AM10/9/19
to deal.II User Group
Hi Denis

thank you very much for pointing out to @balay. His suggestion:

spack install slepc~arpack ^hypre@develop

indeed works. I will prepare a short report on successful installation on CentOS7 through spack, summarizing all these issues. 
I am almost there, but another - hopefully small - problem arises and it is related to the installation of the deal.ii package, thus this forum should be appropriate.
Here is the error message,

==> Installing dealii

==> Searching for binary cache of dealii

==> Warning: No Spack mirrors are currently configured

==> No binary for dealii found: installing from source

==> Using cached archive: /home/deal.ii/spack/var/spack/cache/dealii/dealii-9.1.1.tar.gz

==> Staging archive: /tmp/deal.ii/spack-stage/dealii-9.1.1-3idaq2jucltrqd5z5bdgsdxgfhirhrwx/dealii-9.1.1.tar.gz

==> Created stage in /tmp/deal.ii/spack-stage/dealii-9.1.1-3idaq2jucltrqd5z5bdgsdxgfhirhrwx

==> No patches needed for dealii

==> Building dealii [CMakePackage]

==> Executing phase: 'cmake'

==> Error: ProcessError: Command exited with status 1:

    'cmake' '/tmp/deal.ii/spack-stage/dealii-9.1.1-3idaq2jucltrqd5z5bdgsdxgfhirhrwx/spack-src' '-G' 'Unix Makefiles' '-DCMAKE_INSTALL_PREFIX:PATH=/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/dealii-9.1.1-3idaq2jucltrqd5z5bdgsdxgfhirhrwx' '-DCMAKE_BUILD_TYPE:STRING=DebugRelease' '-DCMAKE_VERBOSE_MAKEFILE:BOOL=ON' '-DCMAKE_INSTALL_RPATH_USE_LINK_PATH:BOOL=FALSE' '-DCMAKE_INSTALL_RPATH:STRING=/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/dealii-9.1.1-3idaq2jucltrqd5z5bdgsdxgfhirhrwx/lib;/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/dealii-9.1.1-3idaq2jucltrqd5z5bdgsdxgfhirhrwx/lib64;/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/openblas-0.3.7-2dvho7dpjd4bndibkwb7hocq2jcjri3a/lib;/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/boost-1.70.0-dqafhnyzp5sbdfre5isyyyr353vzjtgn/lib;/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/suite-sparse-5.3.0-hcb2uveywowaqvnfclinxy43ejj5r6jc/lib;/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/intel-tbb-2019.4-or4oyfysguife7miu6wpj5pvgusr4xrw/lib;/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/zlib-1.2.11-fa7l75havytsbgz77sh6yyzvqgmmm5dj/lib;/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/openmpi-3.1.4-4lzhe2gtz3nzhffn6efu2fzgochphcix/lib;/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/arpack-ng-3.7.0-i5fx7mowpxx7acbasidsfc4r3owcd2vx/lib;/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/assimp-4.0.1-gaj2yfue2mi3pdp5i4d2s3g7fts6mrkg/lib;/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/ginkgo-1.0.0-zsbnkl7a37zhjql2ts4s3eeuq56dueb4/lib;/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/gsl-2.5-f7vcvzuzt3eysbwbdrmhfyakvdpzm7kv/lib;/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/hdf5-1.10.5-lt5jyi3ix6dbrbblku7ygutgek7wg5w2/lib;/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/metis-5.1.0-zepovp3vvqzcirbxoqyb33fg5mm26spe/lib;/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/nanoflann-1.2.3-czda3taau7otp3ls26eezaxhag46gl2v/lib;/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/netcdf-4.7.0-tilgbdk7nwewrjy6yhrou6655uqslsvz/lib;/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/netcdf-cxx-4.2-axbx4ojpxkyvxxshyb2ucxxy6stfmfbq/lib;/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/oce-0.18.3-aobmiazqg5kugtdd6fwujbuevk3w3lcd/lib;/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/p4est-2.2-jfhddkrr4d2rgs4ebmccwx6bd6um4vfa/lib;/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/petsc-3.12.0-7b3mdm63ap32riorneym2mtcmwjlb63s/lib;/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/netlib-scalapack-2.0.2-ztpgqfczbercfgd3ylfyl47mnylz3lyz/lib;/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/slepc-3.12.0-yi7yatd5yz2pjlmxzfjmehw67ucwzyyu/lib;/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/symengine-0.4.0-wn7tujjbrfsywir3u3vkcu3qq47cdiry/lib;/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/trilinos-12.14.1-qqgitozqkocbplh4rqklzdzb5kkdkjpw/lib;/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/suite-sparse-5.3.0-hcb2uveywowaqvnfclinxy43ejj5r6jc/lib64;/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/adol-c-develop-xioth2pegguh6rb6mzfzk7zhvb2kgeue/lib64;/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/arpack-ng-3.7.0-i5fx7mowpxx7acbasidsfc4r3owcd2vx/lib64;/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/muparser-2.2.6.1-uvwxew3watab34neq6akvqia4ptatriw/lib64;/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/sundials-3.2.1-2wz3oscfdibh7yv5rw2dq2ajmj3rvznc/lib64;/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/symengine-0.4.0-wn7tujjbrfsywir3u3vkcu3qq47cdiry/lib64' '-DCMAKE_PREFIX_PATH:STRING=/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/cmake-3.9.4-jy2ih5ctlebz57xqk7kvgzv22tabfbq4;/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/openblas-0.3.7-2dvho7dpjd4bndibkwb7hocq2jcjri3a;/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/boost-1.70.0-dqafhnyzp5sbdfre5isyyyr353vzjtgn;/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/suite-sparse-5.3.0-hcb2uveywowaqvnfclinxy43ejj5r6jc;/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/intel-tbb-2019.4-or4oyfysguife7miu6wpj5pvgusr4xrw;/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/zlib-1.2.11-fa7l75havytsbgz77sh6yyzvqgmmm5dj;/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/openmpi-3.1.4-4lzhe2gtz3nzhffn6efu2fzgochphcix;/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/adol-c-develop-xioth2pegguh6rb6mzfzk7zhvb2kgeue;/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/arpack-ng-3.7.0-i5fx7mowpxx7acbasidsfc4r3owcd2vx;/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/assimp-4.0.1-gaj2yfue2mi3pdp5i4d2s3g7fts6mrkg;/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/ginkgo-1.0.0-zsbnkl7a37zhjql2ts4s3eeuq56dueb4;/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/gmsh-4.2.2-4zcao5w2dwjtzmw6onkajy3d5op6u7cj;/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/gsl-2.5-f7vcvzuzt3eysbwbdrmhfyakvdpzm7kv;/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/hdf5-1.10.5-lt5jyi3ix6dbrbblku7ygutgek7wg5w2;/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/metis-5.1.0-zepovp3vvqzcirbxoqyb33fg5mm26spe;/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/muparser-2.2.6.1-uvwxew3watab34neq6akvqia4ptatriw;/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/nanoflann-1.2.3-czda3taau7otp3ls26eezaxhag46gl2v;/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/netcdf-4.7.0-tilgbdk7nwewrjy6yhrou6655uqslsvz;/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/netcdf-cxx-4.2-axbx4ojpxkyvxxshyb2ucxxy6stfmfbq;/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/oce-0.18.3-aobmiazqg5kugtdd6fwujbuevk3w3lcd;/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/p4est-2.2-jfhddkrr4d2rgs4ebmccwx6bd6um4vfa;/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/petsc-3.12.0-7b3mdm63ap32riorneym2mtcmwjlb63s;/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/netlib-scalapack-2.0.2-ztpgqfczbercfgd3ylfyl47mnylz3lyz;/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/slepc-3.12.0-yi7yatd5yz2pjlmxzfjmehw67ucwzyyu;/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/sundials-3.2.1-2wz3oscfdibh7yv5rw2dq2ajmj3rvznc;/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/symengine-0.4.0-wn7tujjbrfsywir3u3vkcu3qq47cdiry;/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/trilinos-12.14.1-qqgitozqkocbplh4rqklzdzb5kkdkjpw' '-DDEAL_II_COMPONENT_EXAMPLES=ON' '-DDEAL_II_WITH_THREADS:BOOL=ON' '-DBOOST_DIR=/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/boost-1.70.0-dqafhnyzp5sbdfre5isyyyr353vzjtgn' '-DLAPACK_FOUND=true' '-DLAPACK_INCLUDE_DIRS=/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/openblas-0.3.7-2dvho7dpjd4bndibkwb7hocq2jcjri3a/include' '-DLAPACK_LIBRARIES=/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/openblas-0.3.7-2dvho7dpjd4bndibkwb7hocq2jcjri3a/lib/libopenblas.so' '-DUMFPACK_DIR=/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/suite-sparse-5.3.0-hcb2uveywowaqvnfclinxy43ejj5r6jc' '-DZLIB_DIR=/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/zlib-1.2.11-fa7l75havytsbgz77sh6yyzvqgmmm5dj' '-DDEAL_II_ALLOW_BUNDLED=OFF' '-DTBB_DIR=/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/intel-tbb-2019.4-or4oyfysguife7miu6wpj5pvgusr4xrw' '-DDEAL_II_COMPONENT_PYTHON_BINDINGS=OFF' '-DDEAL_II_EXAMPLES_RELDIR=share/deal.II/examples' '-DDEAL_II_DOCREADME_RELDIR=share/deal.II/' '-DDEAL_II_DOCHTML_RELDIR=share/deal.II/doc' '-DDEAL_II_WITH_CUDA=OFF' '-DDEAL_II_WITH_MPI:BOOL=ON' '-DCMAKE_C_COMPILER=/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/openmpi-3.1.4-4lzhe2gtz3nzhffn6efu2fzgochphcix/bin/mpicc' '-DCMAKE_CXX_COMPILER=/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/openmpi-3.1.4-4lzhe2gtz3nzhffn6efu2fzgochphcix/bin/mpic++' '-DCMAKE_Fortran_COMPILER=/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/openmpi-3.1.4-4lzhe2gtz3nzhffn6efu2fzgochphcix/bin/mpif90' '-DGSL_DIR=/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/gsl-2.5-f7vcvzuzt3eysbwbdrmhfyakvdpzm7kv' '-DDEAL_II_WITH_GSL:BOOL=ON' '-DHDF5_DIR=/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/hdf5-1.10.5-lt5jyi3ix6dbrbblku7ygutgek7wg5w2' '-DDEAL_II_WITH_HDF5:BOOL=ON' '-DP4EST_DIR=/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/p4est-2.2-jfhddkrr4d2rgs4ebmccwx6bd6um4vfa' '-DDEAL_II_WITH_P4EST:BOOL=ON' '-DPETSC_DIR=/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/petsc-3.12.0-7b3mdm63ap32riorneym2mtcmwjlb63s' '-DDEAL_II_WITH_PETSC:BOOL=ON' '-DSLEPC_DIR=/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/slepc-3.12.0-yi7yatd5yz2pjlmxzfjmehw67ucwzyyu' '-DDEAL_II_WITH_SLEPC:BOOL=ON' '-DTRILINOS_DIR=/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/trilinos-12.14.1-qqgitozqkocbplh4rqklzdzb5kkdkjpw' '-DDEAL_II_WITH_TRILINOS:BOOL=ON' '-DMETIS_DIR=/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/metis-5.1.0-zepovp3vvqzcirbxoqyb33fg5mm26spe' '-DDEAL_II_WITH_METIS:BOOL=ON' '-DSUNDIALS_DIR=/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/sundials-3.2.1-2wz3oscfdibh7yv5rw2dq2ajmj3rvznc' '-DDEAL_II_WITH_SUNDIALS:BOOL=ON' '-DNANOFLANN_DIR=/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/nanoflann-1.2.3-czda3taau7otp3ls26eezaxhag46gl2v' '-DDEAL_II_WITH_NANOFLANN:BOOL=ON' '-DASSIMP_DIR=/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/assimp-4.0.1-gaj2yfue2mi3pdp5i4d2s3g7fts6mrkg' '-DDEAL_II_WITH_ASSIMP:BOOL=ON' '-DGMSH_DIR=/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/gmsh-4.2.2-4zcao5w2dwjtzmw6onkajy3d5op6u7cj' '-DDEAL_II_WITH_GMSH:BOOL=ON' '-DMUPARSER_DIR=/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/muparser-2.2.6.1-uvwxew3watab34neq6akvqia4ptatriw' '-DDEAL_II_WITH_MUPARSER:BOOL=ON' '-DSYMENGINE_DIR=/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/symengine-0.4.0-wn7tujjbrfsywir3u3vkcu3qq47cdiry' '-DDEAL_II_WITH_SYMENGINE:BOOL=ON' '-DGINKGO_DIR=/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/ginkgo-1.0.0-zsbnkl7a37zhjql2ts4s3eeuq56dueb4' '-DDEAL_II_WITH_GINKGO:BOOL=ON' '-DADOLC_DIR=/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/adol-c-develop-xioth2pegguh6rb6mzfzk7zhvb2kgeue' '-DDEAL_II_WITH_ADOLC=ON' '-DDEAL_II_COMPONENT_DOCUMENTATION=OFF' '-DARPACK_DIR=/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/arpack-ng-3.7.0-i5fx7mowpxx7acbasidsfc4r3owcd2vx' '-DDEAL_II_WITH_ARPACK=ON' '-DDEAL_II_ARPACK_WITH_PARPACK=ON' '-DNETCDF_FOUND=true' '-DNETCDF_LIBRARIES=/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/netcdf-cxx-4.2-axbx4ojpxkyvxxshyb2ucxxy6stfmfbq/lib/libnetcdf_c++.so;/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/netcdf-4.7.0-tilgbdk7nwewrjy6yhrou6655uqslsvz/lib/libnetcdf.so' '-DNETCDF_INCLUDE_DIRS=/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/netcdf-cxx-4.2-axbx4ojpxkyvxxshyb2ucxxy6stfmfbq/include;/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/netcdf-4.7.0-tilgbdk7nwewrjy6yhrou6655uqslsvz/include' '-DSCALAPACK_FOUND=true' '-DSCALAPACK_INCLUDE_DIRS=/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/netlib-scalapack-2.0.2-ztpgqfczbercfgd3ylfyl47mnylz3lyz/include' '-DSCALAPACK_LIBRARIES=/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/netlib-scalapack-2.0.2-ztpgqfczbercfgd3ylfyl47mnylz3lyz/lib/libscalapack.so' '-DDEAL_II_WITH_SCALAPACK=ON' '-DOPENCASCADE_DIR=/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/oce-0.18.3-aobmiazqg5kugtdd6fwujbuevk3w3lcd' '-DDEAL_II_WITH_OPENCASCADE=ON' '-DDEAL_II_WITH_64BIT_INDICES=False' '-DCMAKE_CXX_FLAGS_RELEASE:STRING=-O3' '-DCMAKE_CXX_FLAGS:STRING='


1 error found in build log:

     833    -- Include /tmp/deal.ii/spack-stage/dealii-9.1.1-3idaq2jucltrqd5z5bdgsdxgfhirhrwx/spack-src/cmake/setup_finalize.cmake

     834    -- Performing Test DEAL_II_HAVE_USABLE_FLAGS_DEBUG

     835    -- Performing Test DEAL_II_HAVE_USABLE_FLAGS_DEBUG - Failed

     836    -- Unable to compile a simple test program. Trying to drop "-fuse-ld=gold" from the linker flags.

     837    -- Performing Test DEAL_II_HAVE_USABLE_FLAGS_DEBUG

     838    -- Performing Test DEAL_II_HAVE_USABLE_FLAGS_DEBUG - Failed

  >> 839    CMake Error at cmake/setup_finalize.cmake:137 (MESSAGE):

     840    

     841    

     842        Configuration error: Cannot compile a test program with the final set of

     843        compiler and linker flags:

     844          CXX flags (DEBUG): -pedantic -fPIC -Wall -Wextra -Woverloaded-virtual -Wpointer-arith -Wsign-compare -Wsuggest-override -Wswitch -Wsynth -Wwrite-strings -Wno-placement-new -Wno-deprecated-declarations -Wno-literal-suffix -Wno-psabi -

            Wno-class-memaccess -fopenmp-simd -std=c++17 -fexceptions -Wno-unused-local-typedefs -O0 -ggdb -Wa,--compress-debug-sections

     845          LD flags  (DEBUG): -Wl,--as-needed -rdynamic  -Wl,-rpath -Wl,/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/hwloc-1.11.11-admmx7jd2wn63yvpnbp4secnkvhpmevu/lib -Wl,-rpath -Wl,/home/deal.ii/spack/opt/spack/linux-centos

            7-ivybridge/gcc-9.2.0/openmpi-3.1.4-4lzhe2gtz3nzhffn6efu2fzgochphcix/lib -L/home/deal.ii/packages/gcc/9.2.0/bin/../lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../lib64/ -lgfortran -ggdb


See build log for details:

  /tmp/deal.ii/spack-stage/dealii-9.1.1-3idaq2jucltrqd5z5bdgsdxgfhirhrwx/spack-build-out.txt


I am also attaching the log files that pertain to the compilation error. Thank you to the whole community for the great support.

Alberto
CMakeError.log
spack-build-out.txt
CMakeOutput.log

Alberto Salvadori

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Oct 11, 2019, 2:04:13 PM10/11/19
to deal.II User Group
Sorry to invoke your help again,
since though I am stuck in the very final step, I wonder if anyone can provide some suggestions to the issue below. I really appreciate
Alberto
...

Bruno Turcksin

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Oct 14, 2019, 8:58:46 AM10/14/19
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Alberto,

If you look in the CMakeError.log, you can see what's the real problem:

/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/petsc-3.12.0-7b3mdm63ap32riorneym2mtcmwjlb63s/lib/libpetsc.so:
undefined reference to `hypre_ParCSRMatrixCompleteClone'

Hypre is in the linking line so I am not sure what's the problem. I
don't use PETSc and Hypre so I don't know why you have this error.

Best,

Bruno

Le ven. 11 oct. 2019 à 14:04, Alberto Salvadori
<alberto....@unibs.it> a écrit :
>
> Informativa sulla Privacy: http://www.unibs.it/node/8155
>
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Alberto Salvadori

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Oct 14, 2019, 2:18:50 PM10/14/19
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Thank you, Bruno. 
I did notice the very same error. I do not know either why this error emerges, the installation of hypre, PETSc was part of the spack installation process.
Since all preliminary packages have now been installed with no further errors, I suspect that some settings shall be redefined in the spack system in order to configure
the installation of deal.ii. Whom should I address this question to? 
Alberto  

Alberto Salvadori
 Dipartimento di Ingegneria Meccanica e Industriale (DIMI)
 Universita` di Brescia, via Branze 43, 25123 Brescia
 Italy
 tel 030 3711239
 fax 030 3711312

e-mail:
 alberto....@unibs.it
web-page:
 http://m4lab.unibs.it/faculty.html


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Bruno Turcksin

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Oct 14, 2019, 3:29:09 PM10/14/19
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Alberto,

Le lun. 14 oct. 2019 à 14:18, Alberto Salvadori
<alberto....@unibs.it> a écrit :
>
> Thank you, Bruno.
> I did notice the very same error. I do not know either why this error emerges, the installation of hypre, PETSc was part of the spack installation process.
> Since all preliminary packages have now been installed with no further errors, I suspect that some settings shall be redefined in the spack system in order to configure
> the installation of deal.ii. Whom should I address this question to?
I would report that to spack maybe someone there has seen the same
error. The fact that there are missing symbols should not be specific
to deal.II. I guess the solution for now, is to either switch to the
Trilinos stack or to install petsc and hypre by hand :(

Bruno
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