Spack will be used to manage open source software packages on Fugaku.
Fugaku users can easily use pre-installed packages and built packages based on Spack recipes.
The following list shows the results of building/compiling packages for aarch64 according to the Spack recipes.
Note that the results in this list do not guarantee that each package will work properly.
On the other hand, Fujitsu will provide the following packages compiled with Fujitsu compiler on Fugaku as "external" packages, of which Spack can be aware.
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Compiler | Fujitsu Compiler Fujitsu C/C++ Compiler 4.10.0 tcsds-1.2.38 |
---|---|
Result | Dependency Error |
Failed to install dependency package :
------------------------------------------------
==> Warning: config:terminal_title has been replaced by install_status and is ignored
==> Warning: Failed to initialize repository: '$spack/var/spack/repos/local'.
No repo.yaml found in '$spack/var/spack/repos/local'
To remove the bad repository, run this command:
spack repo rm $spack/var/spack/repos/local
[+] /usr (external gmake-4.2.1-eszqmok6vi6wxcmklx6bqloeidbh25kb)
[+] /vol0003/rccs-sdt/data/a01008/spack-all-test/env-20240227/spack/opt/spack/linux-rhel8-a64fx/fj-4.10.0/zlib-ng-2.1.4-m4nsqgrityww4eqljits3svzi4wynus3
==> Installing graphmap-0.3.0-3kbmv2tybazmtyyoz7ys2k2jkegc7i3q [3/3]
==> No binary for graphmap-0.3.0-3kbmv2tybazmtyyoz7ys2k2jkegc7i3q found: installing from source
==> No patches needed for graphmap
==> graphmap: Executing phase: 'edit'
==> graphmap: Executing phase: 'build'
==> Error: ProcessError: Command exited with status 2:
'make' '-j16'
3 errors found in build log:
127 mkdir -p obj_linux/src/
128 g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src
/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.
1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/"
-Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seql
ib/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c
-fmessage-length=0 -ffreestanding -fopenmp -std=c++11 -Werror=ret
urn-type -pthread -o obj_linux/src/program_parameters.o src/progra
m_parameters.cc
129 mkdir -p obj_linux/src/
130 g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src
/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.
1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/"
-Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seql
ib/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c
-fmessage-length=0 -ffreestanding -fopenmp -std=c++11 -Werror=ret
urn-type -pthread -o obj_linux/src/main.o src/main.cc
131 mkdir -p ./bin/Linux-x64/
132 g++ -static-libgcc -static-libstdc++ -ffreestanding -L"/usr/local/
lib" -o ./bin/Linux-x64/graphmap ./obj_linux/codebase/seqlib/src/li
bs/libdivsufsort-2.0.1-64bit/utils.o ./obj_linux/codebase/gindex/sr
c/main.o ./obj_linux/codebase/argumentparser/src/example.o ./obj_li
nux/codebase/argumentparser/src/argparser.o ./obj_linux/codebase/se
qlib/src/test.o ./obj_linux/codebase/seqlib/src/libs/libdivsufsort-
2.0.1-64bit/sssort.o ./obj_linux/codebase/seqlib/src/libs/libdivsuf
sort-2.0.1-64bit/trsort.o ./obj_linux/codebase/seqlib/src/libs/libd
ivsufsort-2.0.1-64bit/divsufsort.o ./obj_linux/codebase/gindex/src/
minimizer_index/experimental.o ./obj_linux/codebase/gindex/src/mini
mizer_index/compiled_shape.o ./obj_linux/codebase/gindex/src/minimi
zer_index/seed.o ./obj_linux/codebase/gindex/src/minimizer_index/mi
nimizer_generator.o ./obj_linux/codebase/gindex/src/minimizer_index
/index_pos.o ./obj_linux/codebase/gindex/src/minimizer_index/minimi
zer_index.o ./obj_linux/codebase/seqlib/src/utility/utility_general
.o ./obj_linux/codebase/seqlib/src/utility/tictoc.o ./obj_linux/cod
ebase/seqlib/src/utility/evalue_constants.o ./obj_linux/codebase/se
qlib/src/utility/evalue.o ./obj_linux/codebase/seqlib/src/sequences
/sequence_gfa_test.o ./obj_linux/codebase/seqlib/src/sequences/sequ
ence_file.o ./obj_linux/codebase/seqlib/src/sequences/sequence_alig
nment.o ./obj_linux/codebase/seqlib/src/sequences/sequence_gfa.o ./
obj_linux/codebase/seqlib/src/sequences/sequence_alignment_test.o .
/obj_linux/codebase/seqlib/src/sequences/single_sequence.o ./obj_li
nux/codebase/seqlib/src/log_system/log_system.o ./obj_linux/codebas
e/seqlib/src/libs/edlib.o ./obj_linux/codebase/seqlib/src/libs/edli
bcigar.o ./obj_linux/codebase/seqlib/src/libs/opal.o ./obj_linux/sr
c/alignment/alignment.o ./obj_linux/src/alignment/semiglobal.o ./ob
j_linux/src/alignment/transcriptome_mod.o ./obj_linux/src/alignment
/anchored.o ./obj_linux/src/alignment/alignment_wrappers.o ./obj_li
nux/src/alignment/cigargen.o ./obj_linux/src/index/index_util.o ./o
bj_linux/src/containers/path_graph_entry.o ./obj_linux/src/containe
rs/mapping_data.o ./obj_linux/src/containers/vertices.o ./obj_linux
/src/containers/region.o ./obj_linux/src/containers/score_registry.
o ./obj_linux/src/graphmap/experimental.o ./obj_linux/src/graphmap/
lcs_anchored.o ./obj_linux/src/graphmap/region_selection.o ./obj_li
nux/src/graphmap/process_read.o ./obj_linux/src/graphmap/transcript
ome.o ./obj_linux/src/graphmap/lcs_semiglobal.o ./obj_linux/src/gra
phmap/filter_anchors.o ./obj_linux/src/graphmap/graphmap.o ./obj_li
nux/src/graphmap/core_graphmap.o ./obj_linux/src/owler/owler.o ./ob
j_linux/src/owler/lcsk.o ./obj_linux/src/owler/process_read.o ./obj
_linux/src/owler/owler_experimental.o ./obj_linux/src/program_param
eters.o ./obj_linux/src/main.o -lpthread -lgomp -lm -lz
>> 133 ld: cannot find -lstdc++
>> 134 collect2: error: ld returned 1 exit status
>> 135 make: *** [Makefile:120: linux] Error 1
See build log for details:
/data/rccs-sdt/a01008/tmpdir/spack-stage/spack-stage-graphmap-0.3.0-3kbmv2tybazmtyyoz7ys2k2jkegc7i3q/spack-build-out.txt