Installation issue: sda (G100)
Summary
|
|
| Summary |
Spack package build failure |
| Package info |
sda |
| System |
Galileo100 |
| Related |
|
Steps to reproduce the issue
Error message
Error message
==> Installing sda-7.3.3d-sce2eqts3z4ciixnbzxu2wymmxjcw6fs
==> No binary for sda-7.3.3d-sce2eqts3z4ciixnbzxu2wymmxjcw6fs found: installing from source
==> Using cached archive: /g100_work/icei_devel/emathiou/spack-0.18.1/cache/_source-cache/archive/29/295ca0142532759a43375422a4ebc050e15b1c248e45493f5864765a9fe8076f.tgz
==> No patches needed for sda
==> sda: Executing phase: 'edit'
==> sda: Executing phase: 'build'
==> Error: ProcessError: Command exited with status 2:
'make' '-j16'
5 errors found in build log:
50 bd_move.f90
51 check_exclusion.f90
52 main.f90
53 echo "linking sda_flex"
54 linking sda_flex
55 /g100_work/PROJECTS/spack/preprod/01/spack_sources/0.18.1_preprod_base/lib/spack/env/gcc/gfortran -Xlinker --enable-new-dtags -Xlinker -rpath -Xlinker '${ORIGIN}/../lib/' -g -O3 -W -Wall -Wno-target-life
time -cpp -fPIC -Wno-compare-reals -Wno-uninitialized -funroll-all-loops -finline-functions -Wtabs -Wunused-variable -fopenmp -o ../bin/sda_flex csigfun.o mod_force_energy.o mod_set_parameters.o mod_co
mpute_image_charge.o mod_compute_metaldesolv.o mod_compute_force.o mod_compute_force_sdamm.o mod_compute_energy.o mod_compute_energy_sdamm.o mod_hydrodynamics.o mod_compute_analytic_2proteins.o mod_comp
ute_analytic_sdamm.o mod_compute_energy_flex.o mod_init_position.o utils.f90 read_input_file.f90 restart.f90 prepare_grid.f90 prepare_atom_protein.f90 solva.f90 make_exclusion_grid.f90 MainLoop_sda_2pro
teins.f90 MainLoop_sdamm.f90 MainLoop_sda_energy.f90 MainLoop_sda_pmf.f90 MainLoop_sda_2proteins_omp.f90 init_time.f90 compute_distance.f90 check_reaction_pair.f90 eschk.f90 change_conformation.f90 make_
bd_move_2prot.f90 make_bd_move_2prot_timer_excl.f90 make_bd_move_sdamm.f90 bd_move.f90 check_exclusion.f90 main.f90 -Wl,-rpath=../lib -B ../lib -lsda -lstdc++
56 ../lib/libsda.so: undefined reference to log@@GLIBC_2.29' 57 ../lib/libsda.so: undefined reference to exp@@GLIBC_2.29'
58 ../lib/libsda.so: undefined reference to `pow@@GLIBC_2.29'
59 collect2: error: ld returned 1 exit status
60 make: *** [Makefile:258: ../bin/sda_flex] Error 1
See build log for details:
/scratch_local/emathiou/spack-stage-sda-7.3.3d-sce2eqts3z4ciixnbzxu2wymmxjcw6fs/spack-build-out.txt
Information on your system
$ spack debug report
* **Spack:** 0.18.1 (57226fd1f4c6bc8c55fe0bfde9450a326e957f0d)
* **Python:** 3.6.8
* **Platform:** linux-centos8-cascadelake
* **Concretizer:** clingo
Additional information