List of Open Source Software which can be built on Fugaku
 |
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.
|
fastq-screen 0.15.3
| Compiler | Fujitsu Compiler Fujitsu C/C++ Compiler 4.10.0 tcsds-1.2.38 |
|---|---|
| Result | Dependency Error |
Failed Reason
Failed to install dependency package :
------------------------------------------------
qkqbxi5dcv7kbp6bugdcjc5ph6/bin/cmake -E cmake_link_script CMakeFile
s/tbb.dir/link.txt --verbose=1
271 /vol0003/rccs-sdt/data/a01008/spack-all-test/env-20240227/spack/lib
/spack/env/fj/case-insensitive/FCC -fPIC -O3 -DNDEBUG -flto -shared
-Wl,-soname,libtbb.so.12 -o ../../fujitsuclang_7.1_cxx11_64_releas
e/libtbb.so.12.9 CMakeFiles/tbb.dir/address_waiter.cpp.o CMakeFiles
/tbb.dir/allocator.cpp.o CMakeFiles/tbb.dir/arena.cpp.o CMakeFiles/
tbb.dir/arena_slot.cpp.o CMakeFiles/tbb.dir/concurrent_bounded_queu
e.cpp.o CMakeFiles/tbb.dir/dynamic_link.cpp.o CMakeFiles/tbb.dir/ex
ception.cpp.o CMakeFiles/tbb.dir/governor.cpp.o CMakeFiles/tbb.dir/
global_control.cpp.o CMakeFiles/tbb.dir/itt_notify.cpp.o CMakeFiles
/tbb.dir/main.cpp.o CMakeFiles/tbb.dir/market.cpp.o CMakeFiles/tbb.
dir/misc.cpp.o CMakeFiles/tbb.dir/misc_ex.cpp.o CMakeFiles/tbb.dir/
observer_proxy.cpp.o CMakeFiles/tbb.dir/parallel_pipeline.cpp.o CMa
keFiles/tbb.dir/private_server.cpp.o CMakeFiles/tbb.dir/profiling.c
pp.o CMakeFiles/tbb.dir/rml_tbb.cpp.o CMakeFiles/tbb.dir/rtm_mutex.
cpp.o CMakeFiles/tbb.dir/rtm_rw_mutex.cpp.o CMakeFiles/tbb.dir/sema
phore.cpp.o CMakeFiles/tbb.dir/small_object_pool.cpp.o CMakeFiles/t
bb.dir/task.cpp.o CMakeFiles/tbb.dir/task_dispatcher.cpp.o CMakeFil
es/tbb.dir/task_group_context.cpp.o CMakeFiles/tbb.dir/version.cpp.
o CMakeFiles/tbb.dir/queuing_rw_mutex.cpp.o -Wl,-rpath,:::::::::::
:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
::::::::::::::::::::::::::::::::::::::
272 make[2]: Leaving directory '/vol0003/rccs-sdt/data/a01008/tmpdir/sp
ack-stage/spack-stage-intel-tbb-2021.9.0-er5to27rat2j4dv4dizloxefxf
kuusww/spack-build-er5to27'
>> 273 make[1]: *** [CMakeFiles/Makefile2:522: src/tbbmalloc_proxy/CMakeFi
les/tbbmalloc_proxy.dir/all] Error 2
274 make[1]: *** Waiting for unfinished jobs....
275 [ 16%] Linking C executable ../fujitsuclang_7.1_cxx11_64_release/te
st_malloc_pure_c
276 cd /vol0003/rccs-sdt/data/a01008/tmpdir/spack-stage/spack-stage-int
el-tbb-2021.9.0-er5to27rat2j4dv4dizloxefxfkuusww/spack-build-er5to2
7/test && /vol0003/rccs-sdt/data/a01008/spack-all-test/env-20240227
/spack/opt/spack/linux-rhel8-a64fx/fj-4.10.0/cmake-3.27.7-ussgjuqkq
bxi5dcv7kbp6bugdcjc5ph6/bin/cmake -E cmake_link_script CMakeFiles/t
est_malloc_pure_c.dir/link.txt --verbose=1
277 /vol0003/rccs-sdt/data/a01008/spack-all-test/env-20240227/spack/lib
/spack/env/fj/fcc -O3 -DNDEBUG CMakeFiles/test_malloc_pure_c.dir/tb
bmalloc/test_malloc_pure_c.c.o -o ../fujitsuclang_7.1_cxx11_64_rele
ase/test_malloc_pure_c -Wl,-rpath,/vol0003/rccs-sdt/data/a01008/tm
pdir/spack-stage/spack-stage-intel-tbb-2021.9.0-er5to27rat2j4dv4diz
loxefxfkuusww/spack-build-er5to27/fujitsuclang_7.1_cxx11_64_release
../fujitsuclang_7.1_cxx11_64_release/libtbbmalloc.so.2.9
>> 278 ../fujitsuclang_7.1_cxx11_64_release/libtbbmalloc.so.2.9: undefined
reference to `__gxx_personality_v0'
>> 279 ../fujitsuclang_7.1_cxx11_64_release/libtbbmalloc.so.2.9: undefined
reference to `__cxa_begin_catch'
>> 280 ../fujitsuclang_7.1_cxx11_64_release/libtbbmalloc.so.2.9: undefined
reference to `std::terminate()'
>> 281 clang-7: error: linker command failed with exit code 1 (use -v to s
ee invocation)
>> 282 make[2]: *** [test/CMakeFiles/test_malloc_pure_c.dir/build.make:101
: fujitsuclang_7.1_cxx11_64_release/test_malloc_pure_c] Error 1
283 make[2]: Leaving directory '/vol0003/rccs-sdt/data/a01008/tmpdir/sp
ack-stage/spack-stage-intel-tbb-2021.9.0-er5to27rat2j4dv4dizloxefxf
kuusww/spack-build-er5to27'
>> 284 make[1]: *** [CMakeFiles/Makefile2:4062: test/CMakeFiles/test_mallo
c_pure_c.dir/all] Error 2
285 [ 16%] Linking CXX shared library ../fujitsuclang_7.1_cxx11_64_rele
ase/lib_test_malloc_used_by_lib.so
286 cd /vol0003/rccs-sdt/data/a01008/tmpdir/spack-stage/spack-stage-int
el-tbb-2021.9.0-er5to27rat2j4dv4dizloxefxfkuusww/spack-build-er5to2
7/test && /vol0003/rccs-sdt/data/a01008/spack-all-test/env-20240227
/spack/opt/spack/linux-rhel8-a64fx/fj-4.10.0/cmake-3.27.7-ussgjuqkq
bxi5dcv7kbp6bugdcjc5ph6/bin/cmake -E cmake_link_script CMakeFiles/_
test_malloc_used_by_lib.dir/link.txt --verbose=1
287 /vol0003/rccs-sdt/data/a01008/spack-all-test/env-20240227/spack/lib
/spack/env/fj/case-insensitive/FCC -fPIC -O3 -DNDEBUG -shared -Wl,-
soname,lib_test_malloc_used_by_lib.so -o ../fujitsuclang_7.1_cxx11_
64_release/lib_test_malloc_used_by_lib.so CMakeFiles/_test_malloc_u
sed_by_lib.dir/tbbmalloc/test_malloc_used_by_lib.cpp.o -Wl,-rpath,
/vol0003/rccs-sdt/data/a01008/tmpdir/spack-stage/spack-stage-intel-
tbb-2021.9.0-er5to27rat2j4dv4dizloxefxfkuusww/spack-build-er5to27/f
ujitsuclang_7.1_cxx11_64_release ../fujitsuclang_7.1_cxx11_64_relea
se/libtbbmalloc.so.2.9
288 make[2]: Leaving directory '/vol0003/rccs-sdt/data/a01008/tmpdir/sp
ack-stage/spack-stage-intel-tbb-2021.9.0-er5to27rat2j4dv4dizloxefxf
kuusww/spack-build-er5to27'
289 [ 16%] Built target _test_malloc_used_by_lib
290 [ 16%] Linking CXX executable ../fujitsuclang_7.1_cxx11_64_release/
test_malloc_lib_unload
...
325 [ 20%] Linking CXX executable ../fujitsuclang_7.1_cxx11_64_release/
test_scalable_allocator
326 cd /vol0003/rccs-sdt/data/a01008/tmpdir/spack-stage/spack-stage-int
el-tbb-2021.9.0-er5to27rat2j4dv4dizloxefxfkuusww/spack-build-er5to2
7/test && /vol0003/rccs-sdt/data/a01008/spack-all-test/env-20240227
/spack/opt/spack/linux-rhel8-a64fx/fj-4.10.0/cmake-3.27.7-ussgjuqkq
bxi5dcv7kbp6bugdcjc5ph6/bin/cmake -E cmake_link_script CMakeFiles/t
est_scalable_allocator.dir/link.txt --verbose=1
327 /vol0003/rccs-sdt/data/a01008/spack-all-test/env-20240227/spack/lib
/spack/env/fj/case-insensitive/FCC -O3 -DNDEBUG CMakeFiles/test_sca
lable_allocator.dir/tbbmalloc/test_scalable_allocator.cpp.o -o ../f
ujitsuclang_7.1_cxx11_64_release/test_scalable_allocator -Wl,-rpat
h,/vol0003/rccs-sdt/data/a01008/tmpdir/spack-stage/spack-stage-inte
l-tbb-2021.9.0-er5to27rat2j4dv4dizloxefxfkuusww/spack-build-er5to27
/fujitsuclang_7.1_cxx11_64_release ../fujitsuclang_7.1_cxx11_64_rel
ease/libtbbmalloc.so.2.9
328 make[2]: Leaving directory '/vol0003/rccs-sdt/data/a01008/tmpdir/sp
ack-stage/spack-stage-intel-tbb-2021.9.0-er5to27rat2j4dv4dizloxefxf
kuusww/spack-build-er5to27'
329 [ 20%] Built target test_scalable_allocator
330 make[1]: Leaving directory '/vol0003/rccs-sdt/data/a01008/tmpdir/sp
ack-stage/spack-stage-intel-tbb-2021.9.0-er5to27rat2j4dv4dizloxefxf
kuusww/spack-build-er5to27'
>> 331 make: *** [Makefile:169: all] Error 2
See build log for details:
/data/rccs-sdt/a01008/tmpdir/spack-stage/spack-stage-intel-tbb-2021.9.0-er5to27rat2j4dv4dizloxefxfkuusww/spack-build-out.txt
[+] /vol0003/rccs-sdt/data/a01008/spack-all-test/env-20240227/spack/opt/spack/linux-rhel8-a64fx/fj-4.10.0/libtiff-4.5.1-llotejmt2kxuv53dmu7fhwrqrz726ygi
==> Installing htslib-1.17-y6gwptav3s7cgh3q5ui7f65xzrljj2sy [38/45]
==> No binary for htslib-1.17-y6gwptav3s7cgh3q5ui7f65xzrljj2sy found: installing from source
==> Using cached archive: /vol0003/rccs-sdt/data/a01008/spack-all-test/env-20240227/spack/var/spack/cache/_source-cache/archive/76/763779288c40f07646ec7ad98b96c378c739171d162ad98398868783b721839f.tar.bz2
==> No patches needed for htslib
==> htslib: Executing phase: 'autoreconf'
==> htslib: Executing phase: 'configure'
==> htslib: Executing phase: 'build'
==> Error: ProcessError: Command exited with status 2:
'make' '-j16' 'V=1'
1 error found in build log:
85 ==> [2024-03-17-01:36:24.582420] Find (recursive): /data/rccs-sdt/a0
1008/tmpdir/spack-stage/spack-stage-htslib-1.17-y6gwptav3s7cgh3q5ui7
f65xzrljj2sy/spack-src ['libtool']
86 ==> [2024-03-17-01:36:24.665138] Find complete: /data/rccs-sdt/a0100
8/tmpdir/spack-stage/spack-stage-htslib-1.17-y6gwptav3s7cgh3q5ui7f65
xzrljj2sy/spack-src ['libtool']
87 ==> htslib: Executing phase: 'build'
88 ==> [2024-03-17-01:36:24.715684] 'make' '-j16' 'V=1'
89 make: Makefile: Too many levels of symbolic links
90 make: stat: Makefile: Too many levels of symbolic links
>> 91 make: *** No rule to make target 'Makefile'. Stop.
See build log for details:
/data/rccs-sdt/a01008/tmpdir/spack-stage/spack-stage-htslib-1.17-y6gwptav3s7cgh3q5ui7f65xzrljj2sy/spack-build-out.txt
==> Warning: Skipping build of samtools-1.17-uzk2elkrkv44iuaypyqzwm66xp6nbtts since htslib-1.17-y6gwptav3s7cgh3q5ui7f65xzrljj2sy failed
==> Error: fastq-screen-0.15.3-w56wwxjqiemdrr6umtuuiwjksslw6tpi: 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/libgd-2.3.3-is5hfx5ltgpbnqlcji3j46mjw4lnuibm
[+] /vol0003/rccs-sdt/data/a01008/spack-all-test/env-20240227/spack/opt/spack/linux-rhel8-a64fx/fj-4.10.0/perl-gd-2.77-wltgmyzmfwxxlfbqw57xc2q5yehowrki
[+] /vol0003/rccs-sdt/data/a01008/spack-all-test/env-20240227/spack/opt/spack/linux-rhel8-a64fx/fj-4.10.0/perl-gdtextutil-0.86-y7eptluk7ysnetg4cumnutto57p7y2bb
[+] /vol0003/rccs-sdt/data/a01008/spack-all-test/env-20240227/spack/opt/spack/linux-rhel8-a64fx/fj-4.10.0/perl-gdgraph-1.4308-qi2nwnlloxm3n6cwmpd2wlqkiigwmyl5
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