For further information, hoping this can be of use, it turned out that the very same error in slepc installation occurs with gcc@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 Il giorno venerdì 4 ottobre 2019 12:50:24 UTC+2, Alberto Salvadori ha scritto: > > 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 >> >> >> >> >> >> >> >> >> >> -- Informativa sulla Privacy: http://www.unibs.it/node/8155 <http://www.unibs.it/node/8155> -- 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. 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