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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ltr-retriever 2.9.4

Compiler Fujitsu Compiler Fujitsu C/C++ Compiler 4.10.0 tcsds-1.2.38
Result Dependency Error

Failed Reason

Failed to install dependency package :
------------------------------------------------
ack-stage-ncbi-rmblastn-2.14.0-owitwflnqfrle3tcmjk647xctrbxonpx/s
pack-src/c++/ReleaseMT/build/Makefile.rules:100: showalign_unit_t
est.o] Error 1
21135 make[5]: *** Waiting for unfinished jobs....
21136 In file included from /vol0003/rccs-sdt/data/a01008/tmpdir/spack-
stage/spack-stage-ncbi-rmblastn-2.14.0-owitwflnqfrle3tcmjk647xctr
bxonpx/spack-src/c++/src/objtools/align_format/unit_test/tabulari
nof_unit_test.cpp:49:
>> 21137 /vol0003/rccs-sdt/data/a01008/tmpdir/spack-stage/spack-stage-ncbi
-rmblastn-2.14.0-owitwflnqfrle3tcmjk647xctrbxonpx/spack-src/c++/s
rc/objtools/align_format/unit_test/blast_test_util.hpp:76:53: err
or: non-type template argument is not a constant expression
21138 template <int lowest_value = 0, int highest_value = ncbi::CRandom
::GetMax()>
21139 ^~~~~~~~~~~~~
~~~~~~~~~~
21140 /vol0003/rccs-sdt/data/a01008/tmpdir/spack-stage/spack-stage-ncbi
-rmblastn-2.14.0-owitwflnqfrle3tcmjk647xctrbxonpx/spack-src/c++/s
rc/objtools/align_format/unit_test/blast_test_util.hpp:76:53: not
e: non-constexpr function 'GetMax' cannot be used in a constant e
xpression
21141 /vol0003/rccs-sdt/data/a01008/tmpdir/spack-stage/spack-stage-ncbi
-rmblastn-2.14.0-owitwflnqfrle3tcmjk647xctrbxonpx/spack-src/c++/i
nclude/util/random_gen.hpp:295:33: note: declared here
21142 inline CRandom::TValue CRandom::GetMax(void)
21143 ^
21144 In file included from /vol0003/rccs-sdt/data/a01008/tmpdir/spack-
stage/spack-stage-ncbi-rmblastn-2.14.0-owitwflnqfrle3tcmjk647xctr
bxonpx/spack-src/c++/src/objtools/align_format/unit_test/tabulari
nof_unit_test.cpp:49:
>> 21145 /vol0003/rccs-sdt/data/a01008/tmpdir/spack-stage/spack-stage-ncbi
-rmblastn-2.14.0-owitwflnqfrle3tcmjk647xctrbxonpx/spack-src/c++/s
rc/objtools/align_format/unit_test/blast_test_util.hpp:76:37: err
or: template parameter missing a default argument
21146 template <int lowest_value = 0, int highest_value = ncbi::CRandom
::GetMax()>
21147 ^
21148 /vol0003/rccs-sdt/data/a01008/tmpdir/spack-stage/spack-stage-ncbi
-rmblastn-2.14.0-owitwflnqfrle3tcmjk647xctrbxonpx/spack-src/c++/s
rc/objtools/align_format/unit_test/blast_test_util.hpp:76:30: not
e: previous default template argument defined here
21149 template <int lowest_value = 0, int highest_value = ncbi::CRandom
::GetMax()>
21150 ^
21151 2 errors generated.
>> 21152 make[5]: *** [/vol0003/rccs-sdt/data/a01008/tmpdir/spack-stage/sp
ack-stage-ncbi-rmblastn-2.14.0-owitwflnqfrle3tcmjk647xctrbxonpx/s
pack-src/c++/ReleaseMT/build/Makefile.rules:100: blast_test_util.
o] Error 1
21153 2 errors generated.
>> 21154 make[5]: *** [/vol0003/rccs-sdt/data/a01008/tmpdir/spack-stage/sp
ack-stage-ncbi-rmblastn-2.14.0-owitwflnqfrle3tcmjk647xctrbxonpx/s
pack-src/c++/ReleaseMT/build/Makefile.rules:100: aln_printer_unit
_test.o] Error 1
21155 2 errors generated.
>> 21156 make[5]: *** [/vol0003/rccs-sdt/data/a01008/tmpdir/spack-stage/sp
ack-stage-ncbi-rmblastn-2.14.0-owitwflnqfrle3tcmjk647xctrbxonpx/s
pack-src/c++/ReleaseMT/build/Makefile.rules:100: showdefline_unit
_test.o] Error 1
21157 2 errors generated.
>> 21158 make[5]: *** [/vol0003/rccs-sdt/data/a01008/tmpdir/spack-stage/sp
ack-stage-ncbi-rmblastn-2.14.0-owitwflnqfrle3tcmjk647xctrbxonpx/s
pack-src/c++/ReleaseMT/build/Makefile.rules:100: tabularinof_unit
_test.o] Error 1
21159 make[5]: Leaving directory '/vol0003/rccs-sdt/data/a01008/tmpdir/
spack-stage/spack-stage-ncbi-rmblastn-2.14.0-owitwflnqfrle3tcmjk6
47xctrbxonpx/spack-src/c++/ReleaseMT/build/objtools/align_format/
unit_test'
>> 21160 FAILED: src/objtools/align_format/unit_test/Makefile.align_format
_unit_test.app
21161 make[5]: Entering directory '/vol0003/rccs-sdt/data/a01008/tmpdir
/spack-stage/spack-stage-ncbi-rmblastn-2.14.0-owitwflnqfrle3tcmjk
647xctrbxonpx/spack-src/c++/ReleaseMT/build/objtools/align_format
/unit_test'
21162 make[5]: warning: -j16 forced in submake: resetting jobserver mod
e.
21163 /bin/rm -f align_format_unit_test .align_format_unit_test.stamp
21164 make[5]: Leaving directory '/vol0003/rccs-sdt/data/a01008/tmpdir/
spack-stage/spack-stage-ncbi-rmblastn-2.14.0-owitwflnqfrle3tcmjk6
47xctrbxonpx/spack-src/c++/ReleaseMT/build/objtools/align_format/
unit_test'
>> 21165 make[4]: *** [/vol0003/rccs-sdt/data/a01008/tmpdir/spack-stage/sp
ack-stage-ncbi-rmblastn-2.14.0-owitwflnqfrle3tcmjk647xctrbxonpx/s
pack-src/c++/src/build-system/Makefile.meta_l:333: all.nonusr] Er
ror 2
21166 make[4]: Leaving directory '/vol0003/rccs-sdt/data/a01008/tmpdir/
spack-stage/spack-stage-ncbi-rmblastn-2.14.0-owitwflnqfrle3tcmjk6
47xctrbxonpx/spack-src/c++/ReleaseMT/build/objtools/align_format/
unit_test'
>> 21167 make[3]: *** [/vol0003/rccs-sdt/data/a01008/tmpdir/spack-stage/sp
ack-stage-ncbi-rmblastn-2.14.0-owitwflnqfrle3tcmjk647xctrbxonpx/s
pack-src/c++/src/build-system/Makefile.meta_p:129: all_p.real] Er
ror 5
21168 make[3]: Leaving directory '/vol0003/rccs-sdt/data/a01008/tmpdir/
spack-stage/spack-stage-ncbi-rmblastn-2.14.0-owitwflnqfrle3tcmjk6
47xctrbxonpx/spack-src/c++/ReleaseMT/build/objtools/align_format'
>> 21169 make[2]: *** [/vol0003/rccs-sdt/data/a01008/tmpdir/spack-stage/sp
ack-stage-ncbi-rmblastn-2.14.0-owitwflnqfrle3tcmjk647xctrbxonpx/s
pack-src/c++/src/build-system/Makefile.meta_p:129: all_p.real] Er
ror 5
21170 make[2]: Leaving directory '/vol0003/rccs-sdt/data/a01008/tmpdir/
spack-stage/spack-stage-ncbi-rmblastn-2.14.0-owitwflnqfrle3tcmjk6
47xctrbxonpx/spack-src/c++/ReleaseMT/build/objtools'
>> 21171 make[1]: *** [/vol0003/rccs-sdt/data/a01008/tmpdir/spack-stage/sp
ack-stage-ncbi-rmblastn-2.14.0-owitwflnqfrle3tcmjk647xctrbxonpx/s
pack-src/c++/src/build-system/Makefile.meta_p:129: all_p.real] Er
ror 5
21172 make[1]: Leaving directory '/vol0003/rccs-sdt/data/a01008/tmpdir/
spack-stage/spack-stage-ncbi-rmblastn-2.14.0-owitwflnqfrle3tcmjk6
47xctrbxonpx/spack-src/c++/ReleaseMT/build'
>> 21173 make: *** [Makefile:24: all] Error 2

See build log for details:
/data/rccs-sdt/a01008/tmpdir/spack-stage/spack-stage-ncbi-rmblastn-2.14.0-owitwflnqfrle3tcmjk647xctrbxonpx/spack-build-out.txt

==> Warning: Skipping build of repeatmasker-4.0.9-upkzepvoyccvanzqmgyfivna2osktp4d since ncbi-rmblastn-2.14.0-owitwflnqfrle3tcmjk647xctrbxonpx failed
==> Warning: Skipping build of ltr-retriever-2.8.7-uxfaccw2eymuj6go5tklzjrwdbjmk2uy since repeatmasker-4.0.9-upkzepvoyccvanzqmgyfivna2osktp4d failed
==> Installing blast-plus-2.14.1-rcjnudj7aipxtfxbmz4ne42qz4vbdyj5 [24/27]
==> No binary for blast-plus-2.14.1-rcjnudj7aipxtfxbmz4ne42qz4vbdyj5 found: installing from source
==> Using cached archive: /vol0003/rccs-sdt/data/a01008/spack-all-test/env-20240227/spack/var/spack/cache/_source-cache/archive/71/712c2dbdf0fb13cc1c2d4f4ef5dd1ce4b06c3b57e96dfea8f23e6e99f5b1650e.tar.gz
==> No patches needed for blast-plus
==> blast-plus: Executing phase: 'autoreconf'
==> blast-plus: Executing phase: 'configure'
==> Error: ProcessError: Command exited with status 1:
'/vol0003/rccs-sdt/data/a01008/tmpdir/spack-stage/spack-stage-blast-plus-2.14.1-rcjnudj7aipxtfxbmz4ne42qz4vbdyj5/spack-src/c++/configure' '--prefix=/vol0003/rccs-sdt/data/a01008/spack-all-test/env-20240227/spack/opt/spack/linux-rhel8-a64fx/fj-4.10.0/blast-plus-2.14.1-rcjnudj7aipxtfxbmz4ne42qz4vbdyj5' '--with-bin-release' '--without-debug' '--with-mt' '--without-boost' '--with-dll' '--without-static' '--without-static-exe' '--with-jpeg=/vol0003/rccs-sdt/data/a01008/spack-all-test/env-20240227/spack/opt/spack/linux-rhel8-a64fx/fj-4.10.0/libjpeg-turbo-3.0.0-isdeykvaxqsqvht7e4gy4u4and66oeo7' '--with-png=/usr' '--with-freetype=/usr' '--without-hdf5' '--with-z=/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' '--with-bz2=/usr' '--with-lzo=/vol0003/rccs-sdt/data/a01008/spack-all-test/env-20240227/spack/opt/spack/linux-rhel8-a64fx/fj-4.10.0/lzo-2.10-rtnjn5365bl6kfim5eejzfdyomj55ndl' '--with-gnutls=/usr' '--without-openssl' '--with-pcre=/usr' '--with-python=/vol0004/apps/oss/spack-v0.19/opt/spack/linux-rhel8-a64fx/fj-4.8.1/python-3.10.8-7q66snjvhvy7im57hncbgpirmddrb5sk' '--with-perl=/usr'

1 error found in build log:
69 checking whether /vol0003/rccs-sdt/data/a01008/spack-all-test/env-20
240227/spack/lib/spack/env/fj/fcc has an option to discard unneeded
shared libraries... -Wl,--as-needed
70 checking whether /vol0003/rccs-sdt/data/a01008/spack-all-test/env-20
240227/spack/lib/spack/env/fj/fcc has an option to link in whole st
atic archives... -Wl,--whole-archive
71 checking whether _LIBCPP_VERSION is declared... no
72 checking how to enable modern C++ features in /vol0003/rccs-sdt/data
/a01008/spack-all-test/env-20240227/spack/lib/spack/env/fj/case-inse
nsitive/FCC ... -std=gnu++17
73 checking how to enable modern C features in /vol0003/rccs-sdt/data/a
01008/spack-all-test/env-20240227/spack/lib/spack/env/fj/fcc ... -st
d=gnu17 -fgnu89-inline
74 checking for dpkg-architecture... no
>> 75 configure: error: Unable to find static libstdc++ requested by --wit
h-bin-release.

See build log for details:
/data/rccs-sdt/a01008/tmpdir/spack-stage/spack-stage-blast-plus-2.14.1-rcjnudj7aipxtfxbmz4ne42qz4vbdyj5/spack-build-out.txt

==> Error: ltr-retriever-2.8.7-uxfaccw2eymuj6go5tklzjrwdbjmk2uy: Package was not installed
==> Error: Installation request failed. Refer to reported errors for failing package(s).
[+] /vol0003/rccs-sdt/data/a01008/spack-all-test/env-20240227/spack/opt/spack/linux-rhel8-a64fx/fj-4.10.0/cdhit-4.8.1-zld3rbui2l3ejqor4sxq6sdv7lvik34g


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