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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biobambam2 2.0.177

Compiler Arm Compiler 20.1.0
Result Dependency Error

Failed Reason

Failed to install dependency package :
------------------------------------------------
>> 2206 ./.libs/libmaus2.so: undefined reference to `std::filesystem::current_path[abi:cxx11]()'
>> 2207 ./.libs/libmaus2.so: undefined reference to `std::filesystem::__cxx11::path::remove_filename()'
>> 2208 ./.libs/libmaus2.so: undefined reference to `std::filesystem::__cxx11::path::remove_filename()'
>> 2209 ./.libs/libmaus2.so: undefined reference to `std::filesystem::__cxx11::path::_M_split_cmpts()'
>> 2210 ./.libs/libmaus2.so: undefined reference to `std::filesystem::__cxx11::path::_M_split_cmpts()'
>> 2211 ./.libs/libmaus2.so: undefined reference to `std::filesystem::create_directory(std::filesystem::__cxx11::pat
h const&, std::filesystem::__cxx11::path const&)'
>> 2212 ./.libs/libmaus2.so: undefined reference to `std::filesystem::permissions(std::filesystem::__cxx11::path con
st&, std::filesystem::perms, std::filesystem::perm_options)'
>> 2213 ./.libs/libmaus2.so: undefined reference to `std::filesystem::absolute(std::filesystem::__cxx11::path const&
)'
>> 2214 ./.libs/libmaus2.so: undefined reference to `std::filesystem::create_directory(std::filesystem::__cxx11::pat
h const&, std::filesystem::__cxx11::path const&)'
>> 2215 ./.libs/libmaus2.so: undefined reference to `std::filesystem::absolute(std::filesystem::__cxx11::path const&
)'
>> 2216 ./.libs/libmaus2.so: undefined reference to `std::filesystem::permissions(std::filesystem::__cxx11::path con
st&, std::filesystem::perms, std::filesystem::perm_options)'
>> 2217 ./.libs/libmaus2.so: undefined reference to `std::filesystem::create_directory(std::filesystem::__cxx11::pat
h const&, std::filesystem::__cxx11::path const&)'
>> 2218 clang-9: error: linker command failed with exit code 1 (use -v to see invocation)
>> 2219 ./.libs/libmaus2.so: undefined reference to `std::filesystem::permissions(std::filesystem::__cxx11::path con
st&, std::filesystem::perms, std::filesystem::perm_options)'
>> 2220 clang-9: error: linker command failed with exit code 1 (use -v to see invocation)
2221 make[2]: *** [Makefile:6752: testBWTDyn] Error 1
>> 2222 ./.libs/libmaus2.so: undefined reference to `std::filesystem::current_path[abi:cxx11]()'
>> 2223 ./.libs/libmaus2.so: undefined reference to `std::filesystem::__cxx11::path::remove_filename()'
2224 make[2]: *** [Makefile:6770: testBitIO] Error 1
>> 2225 ./.libs/libmaus2.so: undefined reference to `std::filesystem::__cxx11::path::_M_split_cmpts()'
>> 2226 ./.libs/libmaus2.so: undefined reference to `std::filesystem::absolute(std::filesystem::__cxx11::path const&
)'
>> 2227 clang-9: error: linker command failed with exit code 1 (use -v to see invocation)
>> 2228 ./.libs/libmaus2.so: undefined reference to `std::filesystem::create_directory(std::filesystem::__cxx11::pat
h const&, std::filesystem::__cxx11::path const&)'
2229 make[2]: *** [Makefile:6806: testHuffman] Error 1
>> 2230 ./.libs/libmaus2.so: undefined reference to `std::filesystem::permissions(std::filesystem::__cxx11::path con
st&, std::filesystem::perms, std::filesystem::perm_options)'
>> 2231 ./.libs/libmaus2.so: undefined reference to `std::filesystem::current_path[abi:cxx11]()'
>> 2232 ./.libs/libmaus2.so: undefined reference to `std::filesystem::__cxx11::path::remove_filename()'
>> 2233 ./.libs/libmaus2.so: undefined reference to `std::filesystem::__cxx11::path::_M_split_cmpts()'
>> 2234 clang-9: error: linker command failed with exit code 1 (use -v to see invocation)
>> 2235 ./.libs/libmaus2.so: undefined reference to `std::filesystem::absolute(std::filesystem::__cxx11::path const&
)'
>> 2236 ./.libs/libmaus2.so: undefined reference to `std::filesystem::current_path[abi:cxx11]()'
2237 make[2]: *** [Makefile:6746: testAIO] Error 1
>> 2238 ./.libs/libmaus2.so: undefined reference to `std::filesystem::__cxx11::path::remove_filename()'
>> 2239 ./.libs/libmaus2.so: undefined reference to `std::filesystem::create_directory(std::filesystem::__cxx11::pat
h const&, std::filesystem::__cxx11::path const&)'
>> 2240 ./.libs/libmaus2.so: undefined reference to `std::filesystem::__cxx11::path::_M_split_cmpts()'
>> 2241 ./.libs/libmaus2.so: undefined reference to `std::filesystem::permissions(std::filesystem::__cxx11::path con
st&, std::filesystem::perms, std::filesystem::perm_options)'
>> 2242 ./.libs/libmaus2.so: undefined reference to `std::filesystem::absolute(std::filesystem::__cxx11::path const&
)'
>> 2243 ./.libs/libmaus2.so: undefined reference to `std::filesystem::create_directory(std::filesystem::__cxx11::pat
h const&, std::filesystem::__cxx11::path const&)'
>> 2244 ./.libs/libmaus2.so: undefined reference to `std::filesystem::current_path[abi:cxx11]()'
>> 2245 clang-9: error: linker command failed with exit code 1 (use -v to see invocation)
>> 2246 ./.libs/libmaus2.so: undefined reference to `std::filesystem::__cxx11::path::remove_filename()'
>> 2247 ./.libs/libmaus2.so: undefined reference to `std::filesystem::permissions(std::filesystem::__cxx11::path con
st&, std::filesystem::perms, std::filesystem::perm_options)'
>> 2248 ./.libs/libmaus2.so: undefined reference to `std::filesystem::__cxx11::path::_M_split_cmpts()'
2249 make[2]: *** [Makefile:6848: testThreadPoolBgzfRead] Error 1
>> 2250 ./.libs/libmaus2.so: undefined reference to `std::filesystem::absolute(std::filesystem::__cxx11::path const&
)'
>> 2251 ./.libs/libmaus2.so: undefined reference to `std::filesystem::create_directory(std::filesystem::__cxx11::pat
h const&, std::filesystem::__cxx11::path const&)'
>> 2252 ./.libs/libmaus2.so: undefined reference to `std::filesystem::permissions(std::filesystem::__cxx11::path con
st&, std::filesystem::perms, std::filesystem::perm_options)'
>> 2253 clang-9: error: linker command failed with exit code 1 (use -v to see invocation)
>> 2254 ./.libs/libmaus2.so: undefined reference to `std::filesystem::current_path[abi:cxx11]()'
>> 2255 clang-9: error: linker command failed with exit code 1 (use -v to see invocation)
>> 2256 ./.libs/libmaus2.so: undefined reference to `std::filesystem::__cxx11::path::remove_filename()'
>> 2257 ./.libs/libmaus2.so: undefined reference to `std::filesystem::__cxx11::path::_M_split_cmpts()'
2258 make[2]: *** [Makefile:6842: testThreadPoolBgzfDecompress] Error 1
2259 make[2]: *** [Makefile:7022: testbitbtree] Error 1
>> 2260 ./.libs/libmaus2.so: undefined reference to `std::filesystem::absolute(std::filesystem::__cxx11::path const&
)'
>> 2261 ./.libs/libmaus2.so: undefined reference to `std::filesystem::create_directory(std::filesystem::__cxx11::pat
h const&, std::filesystem::__cxx11::path const&)'
>> 2262 ./.libs/libmaus2.so: undefined reference to `std::filesystem::permissions(std::filesystem::__cxx11::path con
st&, std::filesystem::perms, std::filesystem::perm_options)'
>> 2263 clang-9: error: linker command failed with exit code 1 (use -v to see invocation)
2264 make[2]: *** [Makefile:6788: testDNABitWords] Error 1
>> 2265 ./.libs/libmaus2.so: undefined reference to `std::filesystem::current_path[abi:cxx11]()'
>> 2266 ./.libs/libmaus2.so: undefined reference to `std::filesystem::__cxx11::path::remove_filename()'
>> 2267 ./.libs/libmaus2.so: undefined reference to `std::filesystem::__cxx11::path::_M_split_cmpts()'
>> 2268 ./.libs/libmaus2.so: undefined reference to `std::filesystem::current_path[abi:cxx11]()'
>> 2269 ./.libs/libmaus2.so: undefined reference to `std::filesystem::__cxx11::path::remove_filename()'
>> 2270 ./.libs/libmaus2.so: undefined reference to `./.libs/libmaus2.so: undefined reference to `std::filesystem::a
bsolute(std::filesystem::__cxx11::path const&)'
2271 std::filesystem::__cxx11::path::_M_split_cmpts()'
>> 2272 ./.libs/libmaus2.so: undefined reference to `std::filesystem::create_directory(std::filesystem::__cxx11::pat
h const&, std::filesystem::__cxx11::path const&)'
>> 2273 ./.libs/libmaus2.so: undefined reference to `std::filesystem::permissions(std::filesystem::__cxx11::path con
st&, std::filesystem::perms, std::filesystem::perm_options)'
>> 2274 ./.libs/libmaus2.so: undefined reference to `std::filesystem::absolute(std::filesystem::__cxx11::path const&
)'
>> 2275 ./.libs/libmaus2.so: undefined reference to `std::filesystem::create_directory(std::filesystem::__cxx11::pat
h const&, std::filesystem::__cxx11::path const&)'
>> 2276 clang-9: error: linker command failed with exit code 1 (use -v to see invocation)
>> 2277 ./.libs/libmaus2.so: undefined reference to `std::filesystem::permissions(std::filesystem::__cxx11::path con
st&, std::filesystem::perms, std::filesystem::perm_options)'
>> 2278 ./.libs/libmaus2.so: undefined reference to `std::filesystem::current_path[abi:cxx11]()'
>> 2279 ./.libs/libmaus2.so: undefined reference to `std::filesystem::__cxx11::path::remove_filename()'
2280 make[2]: *** [Makefile:6794: testDivSufSort] Error 1
>> 2281 ./.libs/libmaus2.so: undefined reference to `std::filesystem::__cxx11::path::_M_split_cmpts()'
>> 2282 clang-9: error: linker command failed with exit code 1 (use -v to see invocation)
2283 make[2]: *** [Makefile:7028: testbtree] Error 1
>> 2284 ./.libs/libmaus2.so: undefined reference to `std::filesystem::absolute(std::filesystem::__cxx11::path const&
)'
>> 2285 ./.libs/libmaus2.so: undefined reference to `std::filesystem::create_directory(std::filesystem::__cxx11::pat
h const&, std::filesystem::__cxx11::path const&)'
>> 2286 ./.libs/libmaus2.so: undefined reference to `std::filesystem::permissions(std::filesystem::__cxx11::path con
st&, std::filesystem::perms, std::filesystem::perm_options)'
>> 2287 clang-9: error: linker command failed with exit code 1 (use -v to see invocation)
2288 make[2]: *** [Makefile:6800: testFastRead] Error 1
>> 2289 ./.libs/libmaus2.so: undefined reference to `std::filesystem::current_path[abi:cxx11]()'
>> 2290 ./.libs/libmaus2.so: undefined reference to `std::filesystem::__cxx11::path::remove_filename()'
>> 2291 ./.libs/libmaus2.so: undefined reference to `std::filesystem::__cxx11::path::_M_split_cmpts()'
>> 2292 ./.libs/libmaus2.so: undefined reference to `std::filesystem::absolute(std::filesystem::__cxx11::path const&
)'
>> 2293 ./.libs/libmaus2.so: undefined reference to `std::filesystem::create_directory(std::filesystem::__cxx11::pat
h const&, std::filesystem::__cxx11::path const&)'
>> 2294 ./.libs/libmaus2.so: undefined reference to `std::filesystem::permissions(std::filesystem::__cxx11::path con
st&, std::filesystem::perms, std::filesystem::perm_options)'
>> 2295 clang-9: error: linker command failed with exit code 1 (use -v to see invocation)
2296 make[2]: *** [Makefile:6758: testBWTHufDyn] Error 1
>> 2297 ./.libs/libmaus2.so: undefined reference to `std::filesystem::current_path[abi:cxx11]()'
>> 2298 ./.libs/libmaus2.so: undefined reference to `std::filesystem::__cxx11::path::remove_filename()'
>> 2299 ./.libs/libmaus2.so: undefined reference to `std::filesystem::__cxx11::path::_M_split_cmpts()'
>> 2300 ./.libs/libmaus2.so: undefined reference to `std::filesystem::absolute(std::filesystem::__cxx11::path const&
)'
>> 2301 ./.libs/libmaus2.so: undefined reference to `std::filesystem::create_directory(std::filesystem::__cxx11::pat
h const&, std::filesystem::__cxx11::path const&)'
>> 2302 ./.libs/libmaus2.so: undefined reference to `std::filesystem::permissions(std::filesystem::__cxx11::path con
st&, std::filesystem::perms, std::filesystem::perm_options)'
>> 2303 clang-9: error: linker command failed with exit code 1 (use -v to see invocation)
2304 make[2]: *** [Makefile:6836: testThreadPoolBamParse] Error 1
2305 make[2]: Leaving directory '/tmp/r0007/spack-stage/spack-stage-libmaus2-2.0.767-hs2aphkesgu3sajebb46tnjghum6
kznx/spack-src/src'
2306 make[1]: *** [Makefile:677: all-recursive] Error 1
2307 make[1]: Leaving directory '/tmp/r0007/spack-stage/spack-stage-libmaus2-2.0.767-hs2aphkesgu3sajebb46tnjghum6
kznx/spack-src'
2308 make: *** [Makefile:561: all] Error 2

See build log for details:
/tmp/r0007/spack-stage/spack-stage-libmaus2-2.0.767-hs2aphkesgu3sajebb46tnjghum6kznx/spack-build-out.txt

==> Warning: Skipping build of biobambam2-2.0.177-4bi626zu3hekpy2wevm533tatmbx4opg since libmaus2-2.0.767-hs2aphkesgu3sajebb46tnjghum6kznx failed
==> Error: biobambam2-2.0.177-4bi626zu3hekpy2wevm533tatmbx4opg: Package was not installed
==> Error: Installation request failed. Refer to reported errors for failing package(s).


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