Dear Phil, please open a new issue in this group and reference the issue discussion from github.
Kind regards Uwe On Wednesday, June 28, 2017 at 10:28:55 PM UTC+2, Phil H wrote: > > Hi Uwe - I managed to work around the USABLE FLAGS by simply commenting > out the relevant lines of code in the final setup, HOWEVER - > > now the issue is this one: > > imkl is not linking correctly : > https://software.intel.com/en-us/articles/symbol-lookup-error-when-linking-intel-mkl-with-gcc-on-ubuntu > > > I'll attach the error below. > > Seems like I need to apply a -Wl,--no-as-needed linker flag to mkl. Where > would I need to do this in candi do you think? Also, should I add this as > another post? > > > /cvmfs/ > soft.computecanada.ca/easybuild/software/2017/Core/imkl/11.3.4.258/mkl/lib/intel64/libmkl_core.so: > > error: undefined reference to 'isspace' > > /cvmfs/ > soft.computecanada.ca/easybuild/software/2017/Core/imkl/11.3.4.258/mkl/lib/intel64/libmkl_sequential.so: > > error: undefined reference to 'strcmp' > > /cvmfs/ > soft.computecanada.ca/easybuild/software/2017/Core/imkl/11.3.4.258/mkl/lib/intel64/libmkl_core.so: > > error: undefined reference to 'tolower' > > /cvmfs/ > soft.computecanada.ca/easybuild/software/2017/Core/imkl/11.3.4.258/lib/intel64/libirc.so: > > error: undefined reference to '__errno_location' > > /cvmfs/ > soft.computecanada.ca/easybuild/software/2017/Core/imkl/11.3.4.258/mkl/lib/intel64/libmkl_core.so: > > error: undefined reference to 'sched_yield' > > /cvmfs/ > soft.computecanada.ca/easybuild/software/2017/Core/imkl/11.3.4.258/mkl/lib/intel64/libmkl_core.so: > > error: undefined reference to 'free' > > /cvmfs/ > soft.computecanada.ca/easybuild/software/2017/Core/imkl/11.3.4.258/mkl/lib/intel64/libmkl_core.so: > > error: undefined reference to 'malloc' > > /cvmfs/ > soft.computecanada.ca/easybuild/software/2017/Core/imkl/11.3.4.258/mkl/lib/intel64/libmkl_sequential.so: > > error: undefined reference to 'syscall' > > /cvmfs/ > soft.computecanada.ca/easybuild/software/2017/Core/imkl/11.3.4.258/mkl/lib/intel64/libmkl_intel_lp64.so: > > error: undefined reference to 'strrchr' > > /cvmfs/ > soft.computecanada.ca/easybuild/software/2017/Core/imkl/11.3.4.258/mkl/lib/intel64/libmkl_intel_lp64.so: > > error: undefined reference to 'getcwd' > > /cvmfs/ > soft.computecanada.ca/easybuild/software/2017/Core/imkl/11.3.4.258/lib/intel64/libirc.so: > > error: undefined reference to 'strncpy' > > /cvmfs/ > soft.computecanada.ca/easybuild/software/2017/Core/imkl/11.3.4.258/mkl/lib/intel64/libmkl_core.so: > > error: undefined reference to 'stderr' > > /cvmfs/ > soft.computecanada.ca/easybuild/software/2017/Core/imkl/11.3.4.258/mkl/lib/intel64/libmkl_intel_lp64.so: > > error: undefined reference to 'exit' > > /cvmfs/ > soft.computecanada.ca/easybuild/software/2017/Core/imkl/11.3.4.258/mkl/lib/intel64/libmkl_core.so: > > error: undefined reference to 'strdup' > > /cvmfs/ > soft.computecanada.ca/easybuild/software/2017/Core/imkl/11.3.4.258/mkl/lib/intel64/libmkl_core.so: > > error: undefined reference to 'getenv' > > /cvmfs/ > soft.computecanada.ca/easybuild/software/2017/Core/imkl/11.3.4.258/lib/intel64/libirc.so: > > error: undefined reference to 'memmove' > > /cvmfs/ > soft.computecanada.ca/easybuild/software/2017/Core/imkl/11.3.4.258/mkl/lib/intel64/libmkl_core.so: > > error: undefined reference to 'vsnprintf' > > /cvmfs/ > soft.computecanada.ca/easybuild/software/2017/Core/imkl/11.3.4.258/mkl/lib/intel64/libmkl_core.so: > > error: undefined reference to 'strchr' > > /cvmfs/ > soft.computecanada.ca/easybuild/software/2017/Core/imkl/11.3.4.258/mkl/lib/intel64/libmkl_sequential.so: > > error: undefined reference to 'fflush' > > /cvmfs/ > soft.computecanada.ca/easybuild/software/2017/Core/imkl/11.3.4.258/lib/intel64/libirc.so: > > error: undefined reference to 'abort' > > /cvmfs/ > soft.computecanada.ca/easybuild/software/2017/Core/imkl/11.3.4.258/lib/intel64/libirc.so: > > error: undefined reference to 'memcmp' > > /cvmfs/ > soft.computecanada.ca/easybuild/software/2017/Core/imkl/11.3.4.258/mkl/lib/intel64/libmkl_core.so: > > error: undefined reference to 'getpid' > > /cvmfs/ > soft.computecanada.ca/easybuild/software/2017/Core/imkl/11.3.4.258/mkl/lib/intel64/libmkl_sequential.so: > > error: undefined reference to 'fopen' > > /cvmfs/ > soft.computecanada.ca/easybuild/software/2017/Core/imkl/11.3.4.258/mkl/lib/intel64/libmkl_sequential.so: > > error: undefined reference to 'fclose' > > /cvmfs/ > soft.computecanada.ca/easybuild/software/2017/Core/imkl/11.3.4.258/mkl/lib/intel64/libmkl_core.so: > > error: undefined reference to 'fread' > > /cvmfs/ > soft.computecanada.ca/easybuild/software/2017/Core/imkl/11.3.4.258/mkl/lib/intel64/libmkl_core.so: > > error: undefined reference to 'ferror' > > /cvmfs/ > soft.computecanada.ca/easybuild/software/2017/Core/imkl/11.3.4.258/mkl/lib/intel64/libmkl_core.so: > > error: undefined reference to 'fwrite' > > /cvmfs/ > soft.computecanada.ca/easybuild/software/2017/Core/imkl/11.3.4.258/mkl/lib/intel64/libmkl_core.so: > > error: undefined reference to 'clock' > > /cvmfs/ > soft.computecanada.ca/easybuild/software/2017/Core/imkl/11.3.4.258/mkl/lib/intel64/libmkl_core.so: > > error: undefined reference to 'realloc' > > /cvmfs/ > soft.computecanada.ca/easybuild/software/2017/Core/imkl/11.3.4.258/mkl/lib/intel64/libmkl_core.so: > > error: undefined reference to 'calloc' > > /cvmfs/ > soft.computecanada.ca/easybuild/software/2017/Core/imkl/11.3.4.258/mkl/lib/intel64/libmkl_core.so: > > error: undefined reference to 'printf' > > /cvmfs/ > soft.computecanada.ca/easybuild/software/2017/Core/imkl/11.3.4.258/mkl/lib/intel64/libmkl_core.so: > > error: undefined reference to 'abs' > > /cvmfs/ > soft.computecanada.ca/easybuild/software/2017/Core/imkl/11.3.4.258/mkl/lib/intel64/libmkl_core.so: > > error: undefined reference to 'remove' > > /cvmfs/ > soft.computecanada.ca/easybuild/software/2017/Core/imkl/11.3.4.258/mkl/lib/intel64/libmkl_sequential.so: > > error: undefined reference to 'strstr' > > /cvmfs/ > soft.computecanada.ca/easybuild/software/2017/Core/imkl/11.3.4.258/mkl/lib/intel64/libmkl_core.so: > > error: undefined reference to 'time' > > /cvmfs/ > soft.computecanada.ca/easybuild/software/2017/Core/imkl/11.3.4.258/lib/intel64/libirc.so: > > error: undefined reference to 'sscanf' > > /cvmfs/ > soft.computecanada.ca/easybuild/software/2017/Core/imkl/11.3.4.258/mkl/lib/intel64/libmkl_core.so: > > error: undefined reference to 'gettimeofday' > > /cvmfs/ > soft.computecanada.ca/easybuild/software/2017/Core/imkl/11.3.4.258/mkl/lib/intel64/libmkl_core.so: > > error: undefined reference to 'strtod' > > /cvmfs/ > soft.computecanada.ca/easybuild/software/2017/Core/imkl/11.3.4.258/mkl/lib/intel64/libmkl_sequential.so: > > error: undefined reference to 'strtol' > > /cvmfs/ > soft.computecanada.ca/easybuild/software/2017/Core/imkl/11.3.4.258/lib/intel64/libirc.so: > > error: undefined reference to 'ftell' > > /cvmfs/ > soft.computecanada.ca/easybuild/software/2017/Core/imkl/11.3.4.258/lib/intel64/libirc.so: > > error: undefined reference to 'snprintf' > > /cvmfs/ > soft.computecanada.ca/easybuild/software/2017/Core/imkl/11.3.4.258/mkl/lib/intel64/libmkl_core.so: > > error: undefined reference to 'fseek' > > /cvmfs/ > soft.computecanada.ca/easybuild/software/2017/Core/imkl/11.3.4.258/mkl/lib/intel64/libmkl_intel_lp64.so: > > error: undefined reference to 'strncmp' > > /cvmfs/ > soft.computecanada.ca/easybuild/software/2017/Core/imkl/11.3.4.258/mkl/lib/intel64/libmkl_core.so: > > error: undefined reference to 'qsort' > > /cvmfs/ > soft.computecanada.ca/easybuild/software/2017/Core/imkl/11.3.4.258/mkl/lib/intel64/libmkl_sequential.so: > > error: undefined reference to 'fgets' > > /cvmfs/ > soft.computecanada.ca/easybuild/software/2017/Core/imkl/11.3.4.258/lib/intel64/libirc.so: > > error: undefined reference to '__xpg_basename' > > /cvmfs/ > soft.computecanada.ca/easybuild/software/2017/Core/imkl/11.3.4.258/mkl/lib/intel64/libmkl_core.so: > > error: undefined reference to '__ctype_b_loc' > > /cvmfs/ > soft.computecanada.ca/easybuild/software/2017/Core/imkl/11.3.4.258/mkl/lib/intel64/libmkl_sequential.so: > > error: undefined reference to 'sleep' > > /cvmfs/ > soft.computecanada.ca/easybuild/software/2017/Core/imkl/11.3.4.258/lib/intel64/libirc.so: > > error: undefined reference to 'strspn' > > /cvmfs/ > soft.computecanada.ca/easybuild/software/2017/Core/imkl/11.3.4.258/lib/intel64/libirc.so: > > error: undefined reference to 'strtok' > > /cvmfs/ > soft.computecanada.ca/easybuild/software/2017/Core/imkl/11.3.4.258/mkl/lib/intel64/libmkl_core.so: > > error: undefined reference to 'srand' > > /cvmfs/ > soft.computecanada.ca/easybuild/software/2017/Core/imkl/11.3.4.258/mkl/lib/intel64/libmkl_core.so: > > error: undefined reference to 'feof' > > /cvmfs/ > soft.computecanada.ca/easybuild/software/2017/Core/imkl/11.3.4.258/mkl/lib/intel64/libmkl_core.so: > > error: undefined reference to 'rand' > > /cvmfs/ > soft.computecanada.ca/easybuild/software/2017/Core/imkl/11.3.4.258/mkl/lib/intel64/libmkl_core.so: > > error: undefined reference to 'stdout' > > /cvmfs/ > soft.computecanada.ca/easybuild/software/2017/Core/imkl/11.3.4.258/lib/intel64/libirc.so: > > error: undefined reference to '__stack_chk_fail' > > /cvmfs/ > soft.computecanada.ca/easybuild/software/2017/Core/imkl/11.3.4.258/lib/intel64/libirc.so: > > error: undefined reference to '__fprintf_chk' > > /cvmfs/ > soft.computecanada.ca/easybuild/software/2017/Core/imkl/11.3.4.258/lib/intel64/libirc.so: > > error: undefined reference to '__snprintf_chk' > > /cvmfs/ > soft.computecanada.ca/easybuild/software/2017/Core/imkl/11.3.4.258/mkl/lib/intel64/libmkl_intel_lp64.so: > > error: undefined reference to 'atol' > > /cvmfs/ > soft.computecanada.ca/easybuild/software/2017/Core/imkl/11.3.4.258/mkl/lib/intel64/libmkl_core.so: > > error: undefined reference to 'puts' > > /cvmfs/ > soft.computecanada.ca/easybuild/software/2017/Core/imkl/11.3.4.258/mkl/lib/intel64/libmkl_core.so: > > error: undefined reference to '__ctype_toupper_loc' > > /cvmfs/ > soft.computecanada.ca/easybuild/software/2017/Core/imkl/11.3.4.258/mkl/lib/intel64/libmkl_core.so: > > error: undefined reference to 'vfprintf' > > /cvmfs/ > soft.computecanada.ca/easybuild/software/2017/Core/imkl/11.3.4.258/mkl/lib/intel64/libmkl_core.so: > > error: undefined reference to 'catgets' > > /cvmfs/ > soft.computecanada.ca/easybuild/software/2017/Core/imkl/11.3.4.258/mkl/lib/intel64/libmkl_core.so: > > error: undefined reference to 'setenv' > > /cvmfs/ > soft.computecanada.ca/easybuild/software/2017/Core/imkl/11.3.4.258/mkl/lib/intel64/libmkl_core.so: > > error: undefined reference to 'catopen' > > /cvmfs/ > soft.computecanada.ca/easybuild/software/2017/Core/imkl/11.3.4.258/mkl/lib/intel64/libmkl_core.so: > > error: undefined reference to 'strtoul' > > /cvmfs/ > soft.computecanada.ca/easybuild/software/2017/Core/imkl/11.3.4.258/mkl/lib/intel64/libmkl_core.so: > > error: undefined reference to 'getuid' > > /cvmfs/ > soft.computecanada.ca/easybuild/software/2017/Core/imkl/11.3.4.258/mkl/lib/intel64/libmkl_core.so: > > error: undefined reference to '__xstat' > > /cvmfs/ > soft.computecanada.ca/easybuild/software/2017/Core/imkl/11.3.4.258/mkl/lib/intel64/libmkl_core.so: > > error: undefined reference to 'opendir' > > /cvmfs/ > soft.computecanada.ca/easybuild/software/2017/Core/imkl/11.3.4.258/mkl/lib/intel64/libmkl_core.so: > > error: undefined reference to 'readdir' > > /cvmfs/ > soft.computecanada.ca/easybuild/software/2017/Core/imkl/11.3.4.258/mkl/lib/intel64/libmkl_core.so: > > error: undefined reference to 'closedir' > > /cvmfs/ > soft.computecanada.ca/easybuild/software/2017/Core/imkl/11.3.4.258/mkl/lib/intel64/libmkl_intel_lp64.so: > > error: undefined reference to 'readlink' > > /cvmfs/ > soft.computecanada.ca/easybuild/software/2017/Core/imkl/11.3.4.258/mkl/lib/intel64/libmkl_core.so: > > error: undefined reference to 'strtok_r' > > /cvmfs/ > soft.computecanada.ca/easybuild/software/2017/Core/imkl/11.3.4.258/lib/intel64/libirc.so: > > error: undefined reference to 'siglongjmp' > > On Wednesday, June 28, 2017 at 4:26:33 AM UTC-4, Uwe Köcher wrote: >> >> oh dear, never have seen this before, but the discussion is quiet linear >> and it should be resolved in the current master of deal.II... >> >> Maybe try to install the current development version of deal.II, you can >> do it by setting STABLE_BUILD=false in candi.cfg >> >> >> On Wednesday, June 28, 2017 at 9:03:25 AM UTC+2, Phil H wrote: >>> >>> Hi Uwe, I've just ran into this bug as well on the new system - >>> https://github.com/dealii/dealii/issues/3686 >>> >>> >>> >>> On Tuesday, June 27, 2017 at 7:18:35 AM UTC-4, Uwe Köcher wrote: >>>> >>>> Phil, >>>> >>>> I did not see something like this before. You are using a quiet new >>>> version of bash (newer than my bash-4.3.43-4.fc25.x86_64) >>>> >>>> The first lines in the created candi_configure are pasted variable from >>>> the system environment and also candi. >>>> The error occurs for some line I could not reproduce, thus I think that >>>> there is a variable "BASH_FUNC_ml()" in your shell. >>>> Can you try to do the following: >>>> $ unset BASH_FUNC_ml() >>>> $ ./candi.sh >>>> >>>> and report if the error is still there? >>>> >>>> >>>> On Tuesday, June 27, 2017 at 10:58:45 AM UTC+2, Phil H wrote: >>>>> >>>>> Hi there, >>>>> >>>>> I'm installing dealii (then aspect) using candi on a brand new cluster >>>>> and I have an error I have never seen before. >>>>> >>>>> *Building hdf5 1.10.1* >>>>> >>>>> ./candi_configure: line 6: syntax error near unexpected token `(' >>>>> >>>>> ./candi_configure: line 6: `declare -x BASH_FUNC_ml()' >>>>> >>>>> >>>>> Has anyone seen this before? It kills the build, and occurs for any >>>>> package I try. >>>>> >>>>> >>>>> In the candi_configure in hdf5 the offending lines are: >>>>> >>>>> >>>>> declare -x BASH_FUNC_ml() >>>>> >>>>> declare -x BASH_FUNC_module() >>>>> >>>>> >>>>> Modules that are available on the cluster - >>>>> >>>>> >>>>> --------------------------------- Core Modules >>>>> --------------------------------- >>>>> >>>>> gcc/4.8.5 gcc/5.4.0 >>>>> >>>>> >>>>> intel/2016.4 intel/2017.1 >>>>> >>>>> >>>>> >>>>> Bash version is GNU bash, version 4.3.48(1)-release >>>>> >>>>> >>>>> Anyone seen this before? >>>>> >>>>> >>>>> Cheers, >>>>> >>>>> >>>>> Phil >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> -- 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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