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.
|
bsseeker2 2.1.8
| Compiler | Fujitsu Compiler Fujitsu C/C++ Compiler 4.10.0 tcsds-1.2.38 |
|---|---|
| Result | Dependency Error |
Failed Reason
Failed to install dependency package :
------------------------------------------------
4 errors found in build log:
176 /vol0003/rccs-sdt/data/a01008/spack-all-test/env-20240227/spack/l
ib/spack/env/fj/fcc -Wno-unused-result -Wsign-compare -Wunreachable
-code -DNDEBUG -g -fwrapv -O3 -Wall -KPIC -fPIC -I/vol0003/rccs-sdt
/data/a01008/spack-all-test/env-20240227/spack/opt/spack/linux-rhel
8-a64fx/fj-4.10.0/htslib-1.12-kp632r2f5qli56ood7amdbjl2k5obxg7/incl
ude -I/vol0003/rccs-sdt/data/a01008/tmpdir/spack-stage/spack-stage-
py-pysam-0.19.1-75iadzc7tmdsyxumqqebduwi37stfcrt/spack-src/samtools
-I/vol0003/rccs-sdt/data/a01008/tmpdir/spack-stage/spack-stage-py-
pysam-0.19.1-75iadzc7tmdsyxumqqebduwi37stfcrt/spack-src/samtools/lz
4 -I/vol0003/rccs-sdt/data/a01008/tmpdir/spack-stage/spack-stage-py
-pysam-0.19.1-75iadzc7tmdsyxumqqebduwi37stfcrt/spack-src/bcftools -
I/vol0003/rccs-sdt/data/a01008/tmpdir/spack-stage/spack-stage-py-py
sam-0.19.1-75iadzc7tmdsyxumqqebduwi37stfcrt/spack-src/pysam -I/vol0
003/rccs-sdt/data/a01008/tmpdir/spack-stage/spack-stage-py-pysam-0.
19.1-75iadzc7tmdsyxumqqebduwi37stfcrt/spack-src -I/vol0004/apps/oss
/spack-v0.19/opt/spack/linux-rhel8-a64fx/fj-4.8.1/python-3.10.8-7q6
6snjvhvy7im57hncbgpirmddrb5sk/include/python3.10 -c samtools/bam_am
pliconclip.c.pysam.c -o build/temp.linux-aarch64-cpython-310/samtoo
ls/bam_ampliconclip.c.pysam.o -Wno-unused -Wno-strict-prototypes -W
no-sign-compare -Wno-error=declaration-after-statement
177 /vol0003/rccs-sdt/data/a01008/spack-all-test/env-20240227/spack/l
ib/spack/env/fj/fcc -Wno-unused-result -Wsign-compare -Wunreachable
-code -DNDEBUG -g -fwrapv -O3 -Wall -KPIC -fPIC -I/vol0003/rccs-sdt
/data/a01008/spack-all-test/env-20240227/spack/opt/spack/linux-rhel
8-a64fx/fj-4.10.0/htslib-1.12-kp632r2f5qli56ood7amdbjl2k5obxg7/incl
ude -I/vol0003/rccs-sdt/data/a01008/tmpdir/spack-stage/spack-stage-
py-pysam-0.19.1-75iadzc7tmdsyxumqqebduwi37stfcrt/spack-src/samtools
-I/vol0003/rccs-sdt/data/a01008/tmpdir/spack-stage/spack-stage-py-
pysam-0.19.1-75iadzc7tmdsyxumqqebduwi37stfcrt/spack-src/samtools/lz
4 -I/vol0003/rccs-sdt/data/a01008/tmpdir/spack-stage/spack-stage-py
-pysam-0.19.1-75iadzc7tmdsyxumqqebduwi37stfcrt/spack-src/bcftools -
I/vol0003/rccs-sdt/data/a01008/tmpdir/spack-stage/spack-stage-py-py
sam-0.19.1-75iadzc7tmdsyxumqqebduwi37stfcrt/spack-src/pysam -I/vol0
003/rccs-sdt/data/a01008/tmpdir/spack-stage/spack-stage-py-pysam-0.
19.1-75iadzc7tmdsyxumqqebduwi37stfcrt/spack-src -I/vol0004/apps/oss
/spack-v0.19/opt/spack/linux-rhel8-a64fx/fj-4.8.1/python-3.10.8-7q6
6snjvhvy7im57hncbgpirmddrb5sk/include/python3.10 -c samtools/bam_au
x.c.pysam.c -o build/temp.linux-aarch64-cpython-310/samtools/bam_au
x.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -W
no-error=declaration-after-statement
178 /vol0003/rccs-sdt/data/a01008/spack-all-test/env-20240227/spack/l
ib/spack/env/fj/fcc -Wno-unused-result -Wsign-compare -Wunreachable
-code -DNDEBUG -g -fwrapv -O3 -Wall -KPIC -fPIC -I/vol0003/rccs-sdt
/data/a01008/spack-all-test/env-20240227/spack/opt/spack/linux-rhel
8-a64fx/fj-4.10.0/htslib-1.12-kp632r2f5qli56ood7amdbjl2k5obxg7/incl
ude -I/vol0003/rccs-sdt/data/a01008/tmpdir/spack-stage/spack-stage-
py-pysam-0.19.1-75iadzc7tmdsyxumqqebduwi37stfcrt/spack-src/samtools
-I/vol0003/rccs-sdt/data/a01008/tmpdir/spack-stage/spack-stage-py-
pysam-0.19.1-75iadzc7tmdsyxumqqebduwi37stfcrt/spack-src/samtools/lz
4 -I/vol0003/rccs-sdt/data/a01008/tmpdir/spack-stage/spack-stage-py
-pysam-0.19.1-75iadzc7tmdsyxumqqebduwi37stfcrt/spack-src/bcftools -
I/vol0003/rccs-sdt/data/a01008/tmpdir/spack-stage/spack-stage-py-py
sam-0.19.1-75iadzc7tmdsyxumqqebduwi37stfcrt/spack-src/pysam -I/vol0
003/rccs-sdt/data/a01008/tmpdir/spack-stage/spack-stage-py-pysam-0.
19.1-75iadzc7tmdsyxumqqebduwi37stfcrt/spack-src -I/vol0004/apps/oss
/spack-v0.19/opt/spack/linux-rhel8-a64fx/fj-4.8.1/python-3.10.8-7q6
6snjvhvy7im57hncbgpirmddrb5sk/include/python3.10 -c samtools/bam_ca
t.c.pysam.c -o build/temp.linux-aarch64-cpython-310/samtools/bam_ca
t.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -W
no-error=declaration-after-statement
179 /vol0003/rccs-sdt/data/a01008/spack-all-test/env-20240227/spack/l
ib/spack/env/fj/fcc -Wno-unused-result -Wsign-compare -Wunreachable
-code -DNDEBUG -g -fwrapv -O3 -Wall -KPIC -fPIC -I/vol0003/rccs-sdt
/data/a01008/spack-all-test/env-20240227/spack/opt/spack/linux-rhel
8-a64fx/fj-4.10.0/htslib-1.12-kp632r2f5qli56ood7amdbjl2k5obxg7/incl
ude -I/vol0003/rccs-sdt/data/a01008/tmpdir/spack-stage/spack-stage-
py-pysam-0.19.1-75iadzc7tmdsyxumqqebduwi37stfcrt/spack-src/samtools
-I/vol0003/rccs-sdt/data/a01008/tmpdir/spack-stage/spack-stage-py-
pysam-0.19.1-75iadzc7tmdsyxumqqebduwi37stfcrt/spack-src/samtools/lz
4 -I/vol0003/rccs-sdt/data/a01008/tmpdir/spack-stage/spack-stage-py
-pysam-0.19.1-75iadzc7tmdsyxumqqebduwi37stfcrt/spack-src/bcftools -
I/vol0003/rccs-sdt/data/a01008/tmpdir/spack-stage/spack-stage-py-py
sam-0.19.1-75iadzc7tmdsyxumqqebduwi37stfcrt/spack-src/pysam -I/vol0
003/rccs-sdt/data/a01008/tmpdir/spack-stage/spack-stage-py-pysam-0.
19.1-75iadzc7tmdsyxumqqebduwi37stfcrt/spack-src -I/vol0004/apps/oss
/spack-v0.19/opt/spack/linux-rhel8-a64fx/fj-4.8.1/python-3.10.8-7q6
6snjvhvy7im57hncbgpirmddrb5sk/include/python3.10 -c samtools/bam_co
lor.c.pysam.c -o build/temp.linux-aarch64-cpython-310/samtools/bam_
color.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compar
e -Wno-error=declaration-after-statement
180 /vol0003/rccs-sdt/data/a01008/spack-all-test/env-20240227/spack/l
ib/spack/env/fj/fcc -Wno-unused-result -Wsign-compare -Wunreachable
-code -DNDEBUG -g -fwrapv -O3 -Wall -KPIC -fPIC -I/vol0003/rccs-sdt
/data/a01008/spack-all-test/env-20240227/spack/opt/spack/linux-rhel
8-a64fx/fj-4.10.0/htslib-1.12-kp632r2f5qli56ood7amdbjl2k5obxg7/incl
ude -I/vol0003/rccs-sdt/data/a01008/tmpdir/spack-stage/spack-stage-
py-pysam-0.19.1-75iadzc7tmdsyxumqqebduwi37stfcrt/spack-src/samtools
-I/vol0003/rccs-sdt/data/a01008/tmpdir/spack-stage/spack-stage-py-
pysam-0.19.1-75iadzc7tmdsyxumqqebduwi37stfcrt/spack-src/samtools/lz
4 -I/vol0003/rccs-sdt/data/a01008/tmpdir/spack-stage/spack-stage-py
-pysam-0.19.1-75iadzc7tmdsyxumqqebduwi37stfcrt/spack-src/bcftools -
I/vol0003/rccs-sdt/data/a01008/tmpdir/spack-stage/spack-stage-py-py
sam-0.19.1-75iadzc7tmdsyxumqqebduwi37stfcrt/spack-src/pysam -I/vol0
003/rccs-sdt/data/a01008/tmpdir/spack-stage/spack-stage-py-pysam-0.
19.1-75iadzc7tmdsyxumqqebduwi37stfcrt/spack-src -I/vol0004/apps/oss
/spack-v0.19/opt/spack/linux-rhel8-a64fx/fj-4.8.1/python-3.10.8-7q6
6snjvhvy7im57hncbgpirmddrb5sk/include/python3.10 -c samtools/bam_co
nsensus.c.pysam.c -o build/temp.linux-aarch64-cpython-310/samtools/
bam_consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sig
n-compare -Wno-error=declaration-after-statement
181 /vol0003/rccs-sdt/data/a01008/spack-all-test/env-20240227/spack/l
ib/spack/env/fj/fcc -Wno-unused-result -Wsign-compare -Wunreachable
-code -DNDEBUG -g -fwrapv -O3 -Wall -KPIC -fPIC -I/vol0003/rccs-sdt
/data/a01008/spack-all-test/env-20240227/spack/opt/spack/linux-rhel
8-a64fx/fj-4.10.0/htslib-1.12-kp632r2f5qli56ood7amdbjl2k5obxg7/incl
ude -I/vol0003/rccs-sdt/data/a01008/tmpdir/spack-stage/spack-stage-
py-pysam-0.19.1-75iadzc7tmdsyxumqqebduwi37stfcrt/spack-src/samtools
-I/vol0003/rccs-sdt/data/a01008/tmpdir/spack-stage/spack-stage-py-
pysam-0.19.1-75iadzc7tmdsyxumqqebduwi37stfcrt/spack-src/samtools/lz
4 -I/vol0003/rccs-sdt/data/a01008/tmpdir/spack-stage/spack-stage-py
-pysam-0.19.1-75iadzc7tmdsyxumqqebduwi37stfcrt/spack-src/bcftools -
I/vol0003/rccs-sdt/data/a01008/tmpdir/spack-stage/spack-stage-py-py
sam-0.19.1-75iadzc7tmdsyxumqqebduwi37stfcrt/spack-src/pysam -I/vol0
003/rccs-sdt/data/a01008/tmpdir/spack-stage/spack-stage-py-pysam-0.
19.1-75iadzc7tmdsyxumqqebduwi37stfcrt/spack-src -I/vol0004/apps/oss
/spack-v0.19/opt/spack/linux-rhel8-a64fx/fj-4.8.1/python-3.10.8-7q6
6snjvhvy7im57hncbgpirmddrb5sk/include/python3.10 -c samtools/bam_fa
stq.c.pysam.c -o build/temp.linux-aarch64-cpython-310/samtools/bam_
fastq.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compar
e -Wno-error=declaration-after-statement
>> 182 samtools/bam_fastq.c.pysam.c:347:25: error: use of undeclared ident
ifier 'FASTQ_OPT_RNUM'
183 hts_set_opt(fp, FASTQ_OPT_RNUM, 1);
184 ^
>> 185 samtools/bam_fastq.c.pysam.c:350:25: error: use of undeclared ide
ntifier 'FASTQ_OPT_CASAVA'
186 hts_set_opt(fp, FASTQ_OPT_CASAVA, 1);
187 ^
>> 188 samtools/bam_fastq.c.pysam.c:352:21: error: use of undeclared ide
ntifier 'FASTQ_OPT_BARCODE'
189 hts_set_opt(fp, FASTQ_OPT_BARCODE, opts->barcode_tag);
190 ^
>> 191 samtools/bam_fastq.c.pysam.c:363:25: error: use of undeclared ide
ntifier 'FASTQ_OPT_AUX'
192 hts_set_opt(fp, FASTQ_OPT_AUX, tag_list.s);
193 ^
194 4 errors generated.
195 error: command '/vol0003/rccs-sdt/data/a01008/spack-all-test/env-
20240227/spack/lib/spack/env/fj/fcc' failed with exit code 1
196 error: subprocess-exited-with-error
197
See build log for details:
/data/rccs-sdt/a01008/tmpdir/spack-stage/spack-stage-py-pysam-0.19.1-75iadzc7tmdsyxumqqebduwi37stfcrt/spack-build-out.txt
==> Warning: Skipping build of bsseeker2-2.1.8-nkdwtdr4p5lprj52ksesnotpg5ga2ijt since py-pysam-0.19.1-75iadzc7tmdsyxumqqebduwi37stfcrt failed
==> Error: bsseeker2-2.1.8-nkdwtdr4p5lprj52ksesnotpg5ga2ijt: Package was not installed
==> Error: Installation request failed. Refer to reported errors for failing package(s).
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