Hi Alberto,

Try reporting issue on Spack Github and ping @balay .

Denis.

On Friday, October 4, 2019 at 12:50:24 PM UTC+2, Alberto Salvadori wrote:
>
> 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
>
>
> Il giorno martedì 1 ottobre 2019 19:02:43 UTC+2, Alberto Salvadori ha 
> scritto:
>>
>> 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^cmake@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:
>>
>>       openmpi@3.1.4%gcc@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: gcc@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: gcc@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
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>

-- 
The deal.II project is located at http://www.dealii.org/
For mailing list/forum options, see 
https://groups.google.com/d/forum/dealii?hl=en
--- 
You received this message because you are subscribed to the Google Groups 
"deal.II User Group" group.
To unsubscribe from this group and stop receiving emails from it, send an email 
to dealii+unsubscr...@googlegroups.com.
To view this discussion on the web visit 
https://groups.google.com/d/msgid/dealii/c72e5af8-c405-4c2b-97f5-26ee7b292d0f%40googlegroups.com.

Reply via email to