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 2.8.7

Compiler Fujitsu Compiler 4.7.0
Result Dependency Error

Failed Reason

Failed to install dependency package :
------------------------------------------------
-ncbi-rmblastn-2.11.0-m67m2kvjd6ypgi45utehtqxvyf62qfel/spack-src/c
++/ReleaseMT/inc -I/vol0003/rccs-sdt/a01008/spack-stage/spack-stag
e-ncbi-rmblastn-2.11.0-m67m2kvjd6ypgi45utehtqxvyf62qfel/spack-src/
c++/include -DNCBI_BUILD_SESSION_ID=5336184a-8fc1-4f6c-8844-073e9
7e69980 /vol0003/rccs-sdt/a01008/spack-stage/spack-stage-ncbi-rmbl
astn-2.11.0-m67m2kvjd6ypgi45utehtqxvyf62qfel/spack-src/c++/src/cor
elib/ncbidbg.cpp -o ncbidbg.o
>> 1254 /vol0003/rccs-sdt/a01008/spack-stage/spack-stage-ncbi-rmblastn-2.1
1.0-m67m2kvjd6ypgi45utehtqxvyf62qfel/spack-src/c++/src/corelib/ncb
i_system.cpp:1554:36: error: invalid output constraint '=a' in asm
1255 asm volatile("cpuid" : "=a" (r[0]), "=b" (r[1]), "=c"
(r[2]), "=d" (r[3]) : "a" (func_id));
1256 ^
>> 1257 /vol0003/rccs-sdt/a01008/spack-stage/spack-stage-ncbi-rmblastn-2.1
1.0-m67m2kvjd6ypgi45utehtqxvyf62qfel/spack-src/c++/src/corelib/ncb
i_system.cpp:1561:36: error: invalid output constraint '=a' in asm
1258 asm volatile("cpuid" : "=a" (r[0]), "=b" (r[1]), "=c"
(r[2]), "=d" (r[3]) : "a" (func_id), "c" (sub_id));
1259 ^
1260 /vol0003/rccs-sdt/a01008/spack-all-test/env-20220225/spack/lib/spa
ck/env/fj/case-insensitive/FCC -std=gnu++14 -c -Wall -Wno-format
-y2k -pthread -fopenmp -O2 -fPIC -DNDEBUG -D_LARGEFILE_SOURCE
-D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_MT -D_REENTRANT
-D_THREAD_SAFE -I/vol0003/rccs-sdt/a01008/spack-stage/spack-stage
-ncbi-rmblastn-2.11.0-m67m2kvjd6ypgi45utehtqxvyf62qfel/spack-src/c
++/ReleaseMT/inc -I/vol0003/rccs-sdt/a01008/spack-stage/spack-stag
e-ncbi-rmblastn-2.11.0-m67m2kvjd6ypgi45utehtqxvyf62qfel/spack-src/
c++/include -DNCBI_BUILD_SESSION_ID=5336184a-8fc1-4f6c-8844-073e9
7e69980 /vol0003/rccs-sdt/a01008/spack-stage/spack-stage-ncbi-rmbl
astn-2.11.0-m67m2kvjd6ypgi45utehtqxvyf62qfel/spack-src/c++/src/cor
elib/ncbidiag.cpp -o ncbidiag.o
1261 /vol0003/rccs-sdt/a01008/spack-all-test/env-20220225/spack/lib/spa
ck/env/fj/case-insensitive/FCC -std=gnu++14 -c -Wall -Wno-format
-y2k -pthread -fopenmp -O2 -fPIC -DNDEBUG -D_LARGEFILE_SOURCE
-D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_MT -D_REENTRANT
-D_THREAD_SAFE -I/vol0003/rccs-sdt/a01008/spack-stage/spack-stage
-ncbi-rmblastn-2.11.0-m67m2kvjd6ypgi45utehtqxvyf62qfel/spack-src/c
++/ReleaseMT/inc -I/vol0003/rccs-sdt/a01008/spack-stage/spack-stag
e-ncbi-rmblastn-2.11.0-m67m2kvjd6ypgi45utehtqxvyf62qfel/spack-src/
c++/include -DNCBI_BUILD_SESSION_ID=5336184a-8fc1-4f6c-8844-073e9
7e69980 /vol0003/rccs-sdt/a01008/spack-stage/spack-stage-ncbi-rmbl
astn-2.11.0-m67m2kvjd6ypgi45utehtqxvyf62qfel/spack-src/c++/src/cor
elib/ncbidiag_p.cpp -o ncbidiag_p.o
1262 2 errors generated.
>> 1263 make[4]: *** [/vol0003/rccs-sdt/a01008/spack-stage/spack-stage-ncb
i-rmblastn-2.11.0-m67m2kvjd6ypgi45utehtqxvyf62qfel/spack-src/c++/R
eleaseMT/build/Makefile.rules:88: ncbi_system.o] Error 1
1264 make[4]: *** Waiting for unfinished jobs....
1265 /vol0003/rccs-sdt/a01008/spack-stage/spack-stage-ncbi-rmblastn-2.1
1.0-m67m2kvjd6ypgi45utehtqxvyf62qfel/spack-src/c++/src/corelib/ncb
idiag.cpp:873:20: warning: 'GetProperties' is deprecated [-Wdeprec
ated-declarations]
1266 value->GetProperties(CDiagContextThreadData::eProp_Get
); /* NCBI_FAKE_WARNING */
1267 ^
1268 /vol0003/rccs-sdt/a01008/spack-stage/spack-stage-ncbi-rmblastn-2.1
1.0-m67m2kvjd6ypgi45utehtqxvyf62qfel/spack-src/c++/include/corelib
/ncbidiag.hpp:1819:5: note: 'GetProperties' has been explicitly ma
rked deprecated here
1269 NCBI_DEPRECATED TProperties* GetProperties(EGetProperties flag
);

...

1285 ^
1286 /vol0003/rccs-sdt/a01008/spack-stage/spack-stage-ncbi-rmblastn-2.1
1.0-m67m2kvjd6ypgi45utehtqxvyf62qfel/spack-src/c++/include/common/
ncbiconf_impl.h:122:56: note: expanded from macro 'NCBI_LEGACY_DEP
RECATED_0'
1287 # define NCBI_LEGACY_DEPRECATED_0 __attribute__((deprecated)
)
1288 ^
1289 2 warnings generated.
1290 make[4]: Leaving directory '/vol0003/rccs-sdt/a01008/spack-stage/s
pack-stage-ncbi-rmblastn-2.11.0-m67m2kvjd6ypgi45utehtqxvyf62qfel/s
pack-src/c++/ReleaseMT/build/corelib'
>> 1291 FAILED: src/corelib/Makefile.corelib.lib
1292 make[4]: Entering directory '/vol0003/rccs-sdt/a01008/spack-stage/
spack-stage-ncbi-rmblastn-2.11.0-m67m2kvjd6ypgi45utehtqxvyf62qfel/
spack-src/c++/ReleaseMT/build/corelib'
1293 make[4]: warning: -jN forced in submake: disabling jobserver mode.
1294 /bin/rm -f libxncbi.a .xncbi.dep .libxncbi.a.stamp
1295 /bin/rm -f /vol0003/rccs-sdt/a01008/spack-stage/spack-stage-ncbi-r
mblastn-2.11.0-m67m2kvjd6ypgi45utehtqxvyf62qfel/spack-src/c++/Rele
aseMT/lib/libxncbi.a /vol0003/rccs-sdt/a01008/spack-stage/spack-st
age-ncbi-rmblastn-2.11.0-m67m2kvjd6ypgi45utehtqxvyf62qfel/spack-sr
c/c++/ReleaseMT/status/.xncbi.dep \
1296 /vol0003/rccs-sdt/a01008/spack-stage/spack-stage-ncbi-rmblastn
-2.11.0-m67m2kvjd6ypgi45utehtqxvyf62qfel/spack-src/c++/ReleaseMT/l
ib/libxncbi-static.a /vol0003/rccs-sdt/a01008/spack-stage/spack-st
age-ncbi-rmblastn-2.11.0-m67m2kvjd6ypgi45utehtqxvyf62qfel/spack-sr
c/c++/ReleaseMT/status/.xncbi-static.dep
1297 make[4]: Leaving directory '/vol0003/rccs-sdt/a01008/spack-stage/s
pack-stage-ncbi-rmblastn-2.11.0-m67m2kvjd6ypgi45utehtqxvyf62qfel/s
pack-src/c++/ReleaseMT/build/corelib'
>> 1298 make[3]: *** [/vol0003/rccs-sdt/a01008/spack-stage/spack-stage-ncb
i-rmblastn-2.11.0-m67m2kvjd6ypgi45utehtqxvyf62qfel/spack-src/c++/s
rc/build-system/Makefile.meta_l:323: all.nonusr] Error 2
1299 make[3]: Leaving directory '/vol0003/rccs-sdt/a01008/spack-stage/s
pack-stage-ncbi-rmblastn-2.11.0-m67m2kvjd6ypgi45utehtqxvyf62qfel/s
pack-src/c++/ReleaseMT/build/corelib'
>> 1300 make[2]: *** [/vol0003/rccs-sdt/a01008/spack-stage/spack-stage-ncb
i-rmblastn-2.11.0-m67m2kvjd6ypgi45utehtqxvyf62qfel/spack-src/c++/s
rc/build-system/Makefile.meta_l:281: all_l.real] Error 2
1301 make[2]: Leaving directory '/vol0003/rccs-sdt/a01008/spack-stage/s
pack-stage-ncbi-rmblastn-2.11.0-m67m2kvjd6ypgi45utehtqxvyf62qfel/s
pack-src/c++/ReleaseMT/build/corelib'
>> 1302 make[1]: *** [/vol0003/rccs-sdt/a01008/spack-stage/spack-stage-ncb
i-rmblastn-2.11.0-m67m2kvjd6ypgi45utehtqxvyf62qfel/spack-src/c++/s
rc/build-system/Makefile.meta_p:129: all_p.real] Error 5
1303 make[1]: Leaving directory '/vol0003/rccs-sdt/a01008/spack-stage/s
pack-stage-ncbi-rmblastn-2.11.0-m67m2kvjd6ypgi45utehtqxvyf62qfel/s
pack-src/c++/ReleaseMT/build'
1304 make: *** [Makefile:24: all] Error 2

See build log for details:
/home/rccs-sdt/a01008/spack-stage/spack-stage-ncbi-rmblastn-2.11.0-m67m2kvjd6ypgi45utehtqxvyf62qfel/spack-build-out.txt

==> Installing blast-plus-2.12.0-vhg47rkr4n3jc4taoboxeqgstxvpkrsi
==> No binary for blast-plus-2.12.0-vhg47rkr4n3jc4taoboxeqgstxvpkrsi found: installing from source
==> Fetching https://mirror.spack.io/_source-cache/archive/fd/fda3c9c9d488cad6c1880a98a236d842bcf3610e3e702af61f7a48cf0a714b88.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/a01008/spack-stage/spack-stage-blast-plus-2.12.0-vhg47rkr4n3jc4taoboxeqgstxvpkrsi/spack-src/c++/configure' '--prefix=/vol0003/rccs-sdt/a01008/spack-all-test/env-20220225/spack/opt/spack/linux-rhel8-a64fx/fj-4.7.0/blast-plus-2.12.0-vhg47rkr4n3jc4taoboxeqgstxvpkrsi' '--with-bin-release' '--without-debug' '--with-mt' '--without-boost' '--with-dll' '--without-static' '--without-static-exe' '--with-jpeg=/vol0003/rccs-sdt/a01008/spack-all-test/env-20220225/spack/opt/spack/linux-rhel8-a64fx/fj-4.7.0/libjpeg-9d-5ch7pzpaexz2gdf6wuzxkc2v4y3egeoi' '--with-png=/usr' '--with-freetype=/usr' '--without-hdf5' '--with-z=/usr' '--with-bz2=/usr' '--with-lzo=/vol0003/rccs-sdt/a01008/spack-all-test/env-20220225/spack/opt/spack/linux-rhel8-a64fx/fj-4.7.0/lzo-2.10-ilmm6evbqallg652set6a5oa26hhxcqh' '--with-gnutls=/usr' '--without-openssl' '--with-pcre=/usr' '--with-python=/vol0003/rccs-sdt/a01008/opt/python/3.9.9/fj' '--with-perl=/usr'

1 error found in build log:
56 checking whether /vol0003/rccs-sdt/a01008/spack-all-test/env-2022022
5/spack/lib/spack/env/fj/fcc has an option to discard unneeded shar
ed libraries... -Wl,--as-needed
57 checking whether /vol0003/rccs-sdt/a01008/spack-all-test/env-2022022
5/spack/lib/spack/env/fj/fcc has an option to link in whole static
archives... -Wl,--whole-archive
58 checking whether _LIBCPP_VERSION is declared... no
59 checking how to enable C++ '14 features in /vol0003/rccs-sdt/a01008/
spack-all-test/env-20220225/spack/lib/spack/env/fj/case-insensitive/
FCC ... -std=gnu++14
60 checking how to enable C '11 or at least '99 features in /vol0003/rc
cs-sdt/a01008/spack-all-test/env-20220225/spack/lib/spack/env/fj/fcc
... -std=gnu11 -fgnu89-inline
61 checking for dpkg-architecture... no
>> 62 configure: error: Unable to find static libstdc++ requested by --wit
h-bin-release.

See build log for details:
/home/rccs-sdt/a01008/spack-stage/spack-stage-blast-plus-2.12.0-vhg47rkr4n3jc4taoboxeqgstxvpkrsi/spack-build-out.txt

==> Error: ltr-retriever-2.8.7-5qvcijfbavcrizczakrucoyxghmirmev: Package was not installed
==> Error: Installation request failed. Refer to reported errors for failing package(s).


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