List of Open Source Software which can be built on Fugaku

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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.
  • OpenJDK 11
  • Ruby 2.6.5 or later
  • Python2 2.7.15
  • Python3 3.6.8
  • Numpy 1.14.3
  • SciPy 1.0.0
  • Eclipse IDE 2019-09 R Packages
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redundans 0.14a

Compiler Fujitsu Compiler 4.7.0
Result Dependency Error

Failed Reason

Failed to install dependency package :
------------------------------------------------
[+] /vol0003/rccs-sdt/a01008/spack-all-test/env-20220225/spack/opt/spack/linux-rhel8-a64fx/fj-4.7.0/sse2neon-master-43xfuzzf54ktu6pwvlnvcvdudbt35mw2
[+] /usr (external zlib-1.2.11-o3hvygtdcp6vg3bpvsrurq4hgklwtype)
[+] /vol0003/rccs-sdt/a01008/spack-all-test/env-20220225/spack/opt/spack/linux-rhel8-a64fx/fj-4.7.0/gapcloser-1.12-r6-im37jxrvsdjue5eg2guqnerbgngv7kmc
[+] /vol0003/rccs-sdt/a01008/spack-all-test/env-20220225/spack/opt/spack/linux-rhel8-a64fx/fj-4.7.0/last-869-ctsbqlfdwqwla452gf4esvefqbzuy5x3
[+] /vol0003/rccs-sdt/a01008/spack-all-test/env-20220225/spack/opt/spack/linux-rhel8-a64fx/fj-4.7.0/gnuconfig-2021-08-14-ezyvb3gy7i726n45kwb44a4vxle3if3i
[+] /usr (external perl-5.26.3-cfeod657avcbjzlstrxizeulrdfnqb3r)
[+] /vol0003/rccs-sdt/a01008/opt/python/3.9.9/fj (external python-3.9.9-3wcip6atrybofsb566d7pjqwhl76u4dp)
[+] /opt/FJSVxtclanga/tcsds-latest (external fujitsu-ssl2-head-qa7iyj5emttingfmlg3424h3vekiviw3)
==> Installing snap-berkeley-1.0beta.18-e4n3ektd6teikpe53p2ytp7yjor2bt54
==> No binary for snap-berkeley-1.0beta.18-e4n3ektd6teikpe53p2ytp7yjor2bt54 found: installing from source
==> Warning: Missing a source id for sse2neon@master
==> Fetching https://mirror.spack.io/_source-cache/archive/9e/9e8a8dc3f17e3f533d34011afe98316c19cbd70cc8b4830375611e003697daee.tar.gz
==> No patches needed for snap-berkeley
==> snap-berkeley: Executing phase: 'edit'
==> snap-berkeley: Executing phase: 'build'
==> Error: ProcessError: Command exited with status 2:
'make' '-j16'

18 errors found in build log:
7 g++ -O3 -Wno-format -MMD -ISNAPLib -msse -c -o SNAPLib/FASTA.o SNA
PLib/FASTA.cpp
8 g++ -O3 -Wno-format -MMD -ISNAPLib -msse -c -o SNAPLib/BigAlloc.o
SNAPLib/BigAlloc.cpp
9 g++ -O3 -Wno-format -MMD -ISNAPLib -msse -c -o SNAPLib/AlignerCont
ext.o SNAPLib/AlignerContext.cpp
10 g++ -O3 -Wno-format -MMD -ISNAPLib -msse -c -o SNAPLib/GenericFile
_map.o SNAPLib/GenericFile_map.cpp
11 g++ -O3 -Wno-format -MMD -ISNAPLib -msse -c -o SNAPLib/Util.o SNAP
Lib/Util.cpp
12 g++ -O3 -Wno-format -MMD -ISNAPLib -msse -c -o SNAPLib/SeedSequenc
er.o SNAPLib/SeedSequencer.cpp
>> 13 g++: error: unrecognized command line option '-msse'; did you mean '
-fdse'?
14 g++ -O3 -Wno-format -MMD -ISNAPLib -msse -c -o SNAPLib/GenericFile
.o SNAPLib/GenericFile.cpp
>> 15 g++: error: unrecognized command line option '-msse'; did you mean '
-fdse'?
>> 16 g++: error: unrecognized command line option '-msse'; did you mean '
-fdse'?
>> 17 g++: error: unrecognized command line option '-msse'; did you mean '
-fdse'?
>> 18 g++: error: unrecognized command line option '-msse'; did you mean '
-fdse'?
>> 19 g++: error: unrecognized command line option '-msse'; did you mean '
-fdse'?
>> 20 make: *** [<builtin>: SNAPLib/FASTQ.o] Error 1
21 make: *** Waiting for unfinished jobs....
>> 22 make: *** [<builtin>: SNAPLib/ParallelTask.o] Error 1
>> 23 make: *** [<builtin>: SNAPLib/FASTA.o] Error 1
>> 24 make: *** [<builtin>: SNAPLib/BigAlloc.o] Error 1
>> 25 make: *** [<builtin>: SNAPLib/AlignerContext.o] Error 1
>> 26 make: *** [<builtin>: SNAPLib/GenericFile_map.o] Error 1
>> 27 g++: error: unrecognized command line option '-msse'; did you mean '
-fdse'?
>> 28 make: *** [<builtin>: SNAPLib/Util.o] Error 1
>> 29 g++: error: unrecognized command line option '-msse'; did you mean '
-fdse'?
>> 30 make: *** [<builtin>: SNAPLib/SeedSequencer.o] Error 1
>> 31 g++: error: unrecognized command line option '-msse'; did you mean '
-fdse'?
>> 32 make: *** [<builtin>: SNAPLib/GenericFile.o] Error 1

See build log for details:
/home/rccs-sdt/a01008/spack-stage/spack-stage-snap-berkeley-1.0beta.18-e4n3ektd6teikpe53p2ytp7yjor2bt54/spack-build-out.txt

[+] /vol0003/rccs-sdt/a01008/spack-all-test/env-20220225/spack/opt/spack/linux-rhel8-a64fx/fj-4.7.0/bwa-0.7.17-gex76yibcr66f7hv5atb6wj676ld2zcj
[+] /vol0003/rccs-sdt/a01008/spack-all-test/env-20220225/spack/opt/spack/linux-rhel8-a64fx/fj-4.7.0/perl-module-build-0.4224-rffcqbqsimvmylgezexantsbf7l5ksta
[+] /vol0003/rccs-sdt/a01008/spack-all-test/env-20220225/spack/opt/spack/linux-rhel8-a64fx/fj-4.7.0/parallel-20210922-gdzdlmg4tl7qji5haitu4nzsdiydz5bw
[+] /vol0003/rccs-sdt/a01008/spack-all-test/env-20220225/spack/opt/spack/linux-rhel8-a64fx/fj-4.7.0/py-setuptools-58.2.0-nwtt7d5cczfaezzecmrcr4swo63tvrg2
[+] /vol0003/rccs-sdt/a01008/spack-all-test/env-20220225/spack/opt/spack/linux-rhel8-a64fx/fj-4.7.0/perl-perl4-corelibs-0.004-vlbnwa6djnsz6nkndcm6kmaebocqjhe4
[+] /vol0003/rccs-sdt/a01008/spack-all-test/env-20220225/spack/opt/spack/linux-rhel8-a64fx/fj-4.7.0/py-cython-0.29.24-rmuycsh3hdsfbp3ffdahdadzgeju5kfs
[+] /vol0003/rccs-sdt/a01008/spack-all-test/env-20220225/spack/opt/spack/linux-rhel8-a64fx/fj-4.7.0/py-fastaindex-0.11rc7-limr2po6hgm2z6ns5cnkmpoj64s5cxph
==> Installing sspace-standard-3.0-r6chm6raayerozanvho5bakt2gc6xbrd
==> No binary for sspace-standard-3.0-r6chm6raayerozanvho5bakt2gc6xbrd found: installing from source
==> Warning: Skipping build of redundans-0.14a-onfuml7xt36cbojz5c56mj55utrsihax since snap-berkeley-1.0beta.18-e4n3ektd6teikpe53p2ytp7yjor2bt54 failed
==> Error: FetchError: Manual download is required for sspace-standard. Refer to https://www.baseclear.com/genomics/bioinformatics/basetools/SSPACE for download instructions.

/vol0003/rccs-sdt/a01008/spack-all-test/env-20220225/spack/lib/spack/spack/package.py:1387, in do_fetch:
1384
1385 self.stage.create()
1386 err_msg = None if not self.manual_download else self.download_instr
>> 1387 start_time = time.time()
1388 self.stage.fetch(mirror_only, err_msg=err_msg)
1389 self._fetch_time = time.time() - start_time
1390

==> Installing py-numpy-1.21.3-eopspnavmocj2cziofoszo4vonyhfseh
==> No binary for py-numpy-1.21.3-eopspnavmocj2cziofoszo4vonyhfseh found: installing from source
==> Using cached archive: /vol0003/rccs-sdt/a01008/spack-all-test/env-20220225/spack/var/spack/cache/_source-cache/archive/63/63571bb7897a584ca3249c86dd01c10bcb5fe4296e3568b2e9c1a55356b6410e.zip
==> Applied patch /vol0003/rccs-sdt/a01008/spack-all-test/env-20220225/spack/var/spack/repos/builtin/packages/py-numpy/check_executables.patch
==> py-numpy: Executing phase: 'build'
==> Error: ProcessError: Command exited with status 1:
'/vol0003/rccs-sdt/a01008/opt/python/3.9.9/fj/bin/python3.9' '-s' 'setup.py' '--no-user-cfg' 'build'
See build log for details:
/home/rccs-sdt/a01008/spack-stage/spack-stage-py-numpy-1.21.3-eopspnavmocj2cziofoszo4vonyhfseh/spack-build-out.txt

==> Error: redundans-0.14a-onfuml7xt36cbojz5c56mj55utrsihax: Package was not installed
==> Error: Installation request failed. Refer to reported errors for failing package(s).
[+] /vol0003/rccs-sdt/a01008/spack-all-test/env-20220225/spack/opt/spack/linux-rhel8-a64fx/fj-4.7.0/py-pyscaf-0.12a4-6vvjskcvg3zeoowrr2wmxqtthdutwfeg


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