error during installation with spack on CentOS7

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

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

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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

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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:

https://github.com/spack/spack-configs

https://github.com/eth-cscs/production/tree/master/spack/daint

https://ceed.exascaleproject.org/ceed-1.0/

https://gitlab.dkrz.de/m300488/icon-bootstrap/tree/master/config/sites

Denis.

Alberto Salvadori

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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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Alberto Salvadori

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Oct 2, 2019, 7:24:32 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 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

unread,

Oct 2, 2019, 8:41:47 AM10/2/19

to deal.II User Group

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

to dea...@googlegroups.com

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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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

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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

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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

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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

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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 :
>

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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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