| Back to --- experimental! --- GPU-enabled build/check report for BioC 3.21 Report updated every hour |
This page was generated on 2025-04-09 14:35 -0400 (Wed, 09 Apr 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| biocgpu | Linux (Ubuntu 24.04.2 LTS) | x86_64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 96 |
| kakapo1 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | R Under development (unstable) (2025-02-26 r87830) -- "Unsuffered Consequences" | 59 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 1/1 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | ||||||||
| RbowtieCuda 0.99.0 (landing page) Franck RICHARD
| biocgpu | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | OK | ||||||||
| kakapo1 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
|
To the developers/maintainers of the RbowtieCuda package: - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: RbowtieCuda |
| Version: 0.99.0 |
| Command: /home/biocbuild/bbs-3.21-bioc-gpu/R/bin/R CMD check --install=check:RbowtieCuda.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc-gpu/R/site-library --timings RbowtieCuda_0.99.0.tar.gz |
| StartedAt: 2025-04-09 14:18:50 -0400 (Wed, 09 Apr 2025) |
| EndedAt: 2025-04-09 14:24:20 -0400 (Wed, 09 Apr 2025) |
| EllapsedTime: 330.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: RbowtieCuda.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### /home/biocbuild/bbs-3.21-bioc-gpu/R/bin/R CMD check --install=check:RbowtieCuda.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc-gpu/R/site-library --timings RbowtieCuda_0.99.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-bioc-gpu/meat/RbowtieCuda.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘RbowtieCuda/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RbowtieCuda’ version ‘0.99.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
.BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘RbowtieCuda’ can be installed ... OK
* checking installed package size ... INFO
installed size is 43.7Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub records with missing/empty fields:
Record: 1 Field(s): ORGANIZATION
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... INFO
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking compiled code ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/home/biocbuild/bbs-3.21-bioc-gpu/meat/RbowtieCuda.Rcheck/00check.log’
for details.
RbowtieCuda.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc-gpu/R/bin/R CMD INSTALL RbowtieCuda ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc-gpu/R/site-library’ * installing *source* package ‘RbowtieCuda’ ... ** this is package ‘RbowtieCuda’ version ‘0.99.0’ ** using staged installation ** libs cd "../src/nvbio/build" && rm -f CMakeCache.txt && cmake .. -- The C compiler identification is GNU 13.3.0 -- The CXX compiler identification is GNU 13.3.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found CUDAToolkit: /software/u24/nvhpc/24.7/Linux_x86_64/24.7/cuda/12.5/targets/x86_64-linux/include (found version "12.5.82") -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- Building Release -- Found libcudacxx: /usr/share/cmake/libcudacxx/libcudacxx-config.cmake (found suitable version "1.9.0.0", minimum required is "1.8.0") -- Found Thrust: /usr/share/cmake/thrust/thrust-config.cmake (found version "2.0.1.0") -- Found CUB: /usr/share/cmake/cub/cub-config.cmake (found version "2.0.1.0") -- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE) -- The CUDA compiler identification is NVIDIA 12.5.82 -- Detecting CUDA compiler ABI info -- Detecting CUDA compiler ABI info - done -- Check for working CUDA compiler: /software/u24/nvhpc/24.7/Linux_x86_64/24.7/compilers/bin/nvcc - skipped -- Detecting CUDA compile features -- Detecting CUDA compile features - done -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Looking for sys/types.h -- Looking for sys/types.h - found -- Looking for stdint.h -- Looking for stdint.h - found -- Looking for stddef.h -- Looking for stddef.h - found -- Check size of off64_t -- Check size of off64_t - done -- Looking for fseeko -- Looking for fseeko - found -- Looking for unistd.h -- Looking for unistd.h - found -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Configuring done (4.9s) -- Generating done (0.0s) -- Build files have been written to: /home/biocbuild/bbs-3.21-bioc-gpu/meat/RbowtieCuda/src/nvbio/build (cd "../src/nvbio/build" && make) make[1]: Entering directory '/home/biocbuild/bbs-3.21-bioc-gpu/meat/RbowtieCuda/src/nvbio/build' make[2]: Entering directory '/home/biocbuild/bbs-3.21-bioc-gpu/meat/RbowtieCuda/src/nvbio/build' make[3]: Entering directory '/home/biocbuild/bbs-3.21-bioc-gpu/meat/RbowtieCuda/src/nvbio/build' make[3]: Entering directory '/home/biocbuild/bbs-3.21-bioc-gpu/meat/RbowtieCuda/src/nvbio/build' make[3]: Entering directory '/home/biocbuild/bbs-3.21-bioc-gpu/meat/RbowtieCuda/src/nvbio/build' make[3]: Entering directory '/home/biocbuild/bbs-3.21-bioc-gpu/meat/RbowtieCuda/src/nvbio/build' make[3]: Entering directory '/home/biocbuild/bbs-3.21-bioc-gpu/meat/RbowtieCuda/src/nvbio/build' make[3]: Entering directory '/home/biocbuild/bbs-3.21-bioc-gpu/meat/RbowtieCuda/src/nvbio/build' make[3]: Entering directory '/home/biocbuild/bbs-3.21-bioc-gpu/meat/RbowtieCuda/src/nvbio/build' make[3]: Leaving directory '/home/biocbuild/bbs-3.21-bioc-gpu/meat/RbowtieCuda/src/nvbio/build' make[3]: Leaving directory '/home/biocbuild/bbs-3.21-bioc-gpu/meat/RbowtieCuda/src/nvbio/build' make[3]: Leaving directory '/home/biocbuild/bbs-3.21-bioc-gpu/meat/RbowtieCuda/src/nvbio/build' make[3]: Leaving directory '/home/biocbuild/bbs-3.21-bioc-gpu/meat/RbowtieCuda/src/nvbio/build' make[3]: Entering directory '/home/biocbuild/bbs-3.21-bioc-gpu/meat/RbowtieCuda/src/nvbio/build' make[3]: Leaving directory '/home/biocbuild/bbs-3.21-bioc-gpu/meat/RbowtieCuda/src/nvbio/build' make[3]: Entering directory '/home/biocbuild/bbs-3.21-bioc-gpu/meat/RbowtieCuda/src/nvbio/build' make[3]: Leaving directory '/home/biocbuild/bbs-3.21-bioc-gpu/meat/RbowtieCuda/src/nvbio/build' make[3]: Entering directory '/home/biocbuild/bbs-3.21-bioc-gpu/meat/RbowtieCuda/src/nvbio/build' make[3]: Entering directory '/home/biocbuild/bbs-3.21-bioc-gpu/meat/RbowtieCuda/src/nvbio/build' make[3]: Entering directory '/home/biocbuild/bbs-3.21-bioc-gpu/meat/RbowtieCuda/src/nvbio/build' make[3]: Leaving directory '/home/biocbuild/bbs-3.21-bioc-gpu/meat/RbowtieCuda/src/nvbio/build' make[3]: Entering directory '/home/biocbuild/bbs-3.21-bioc-gpu/meat/RbowtieCuda/src/nvbio/build' make[3]: Entering directory '/home/biocbuild/bbs-3.21-bioc-gpu/meat/RbowtieCuda/src/nvbio/build' [ 1%] Building C object contrib/lz4/CMakeFiles/lz4.dir/lz4.c.o [ 2%] Building C object contrib/zlib-1.2.7/CMakeFiles/zlib.dir/adler32.c.o [ 3%] Building C object contrib/zlib-1.2.7/CMakeFiles/zlibstatic.dir/trees.c.o [ 4%] Building C object contrib/zlib-1.2.7/CMakeFiles/zlib.dir/gzread.c.o [ 5%] Building C object contrib/lz4/CMakeFiles/lz4.dir/lz4hc.c.o [ 1%] Building C object contrib/zlib-1.2.7/CMakeFiles/zlibstatic.dir/deflate.c.o [ 1%] Building C object contrib/zlib-1.2.7/CMakeFiles/zlib.dir/compress.c.o [ 1%] Building C object contrib/zlib-1.2.7/CMakeFiles/zlibstatic.dir/adler32.c.o [ 1%] Building C object contrib/zlib-1.2.7/CMakeFiles/zlib.dir/gzclose.c.o [ 6%] Building C object contrib/lz4/CMakeFiles/lz4.dir/lz4frame.c.o 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48%] Building CUDA object nvbio/CMakeFiles/nvbio.dir/basic/timer.cu.o [ 49%] Building CUDA object nvbio/CMakeFiles/nvbio.dir/basic/exceptions.cu.o make[3]: Leaving directory '/home/biocbuild/bbs-3.21-bioc-gpu/meat/RbowtieCuda/src/nvbio/build' [ 49%] Building CUDA object nvbio/CMakeFiles/nvbio.dir/basic/mmap.cu.o [ 51%] Building CUDA object nvbio/CMakeFiles/nvbio.dir/basic/cuda/sort.cu.o [ 51%] Building CUDA object nvbio/CMakeFiles/nvbio.dir/basic/system.cu.o [ 52%] Building CUDA object nvbio/CMakeFiles/nvbio.dir/basic/html.cu.o [ 53%] Building CUDA object nvbio/CMakeFiles/nvbio.dir/basic/threads.cu.o [ 54%] Building CUDA object nvbio/CMakeFiles/nvbio.dir/basic/cuda/scan_test.cu.o [ 54%] Building CUDA object nvbio/CMakeFiles/nvbio.dir/fmindex/paged_text.cu.o [ 55%] Building CUDA object nvbio/CMakeFiles/nvbio.dir/sufsort/sufsort_priv.cu.o [ 56%] Building CUDA object nvbio/CMakeFiles/nvbio.dir/sufsort/file_bwt.cu.o [ 56%] Built target crcstatic [ 56%] Building CUDA object 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nvBowtie/CMakeFiles/nvBowtie.dir/nvBowtie.cu.o [ 62%] Building CUDA object nvbio-test/CMakeFiles/nvbio-test.dir/alignment_test.cu.o [ 63%] Building CUDA object nvbio-test/CMakeFiles/nvbio-test.dir/bloom_filter_test.cu.o [ 63%] Building CUDA object nvBowtie/CMakeFiles/nvBowtie.dir/bowtie2/cuda/aligner_best_approx_ed.cu.o [ 64%] Building CUDA object nvBowtie/CMakeFiles/nvBowtie.dir/bowtie2/cuda/aligner_all_ed.cu.o [ 64%] Building CUDA object nvbio-test/CMakeFiles/nvbio-test.dir/alloc_test.cu.o [ 65%] Building CUDA object nvBWT/CMakeFiles/nvBWT.dir/nvBWT.cu.o [ 66%] Building CUDA object nvBowtie/CMakeFiles/nvBowtie.dir/bowtie2/cuda/aligner_best_approx_paired_ed.cu.o [ 66%] Building CUDA object nvBowtie/CMakeFiles/nvBowtie.dir/bowtie2/quality_coeffs.cu.o [ 66%] Building CUDA object nvBowtie/CMakeFiles/nvBowtie.dir/bowtie2/cuda/aligner_best_approx_paired_sw.cu.o [ 67%] Building CUDA object nvbio-test/CMakeFiles/nvbio-test.dir/fasta_test.cu.o [ 68%] Building CUDA object nvBowtie/CMakeFiles/nvBowtie.dir/bowtie2/cuda/aligner_all_sw.cu.o [ 69%] Building CUDA object nvBowtie/CMakeFiles/nvBowtie.dir/bowtie2/cuda/aligner_best_approx_sw.cu.o [ 70%] Building CUDA object nvbio-test/CMakeFiles/nvbio-test.dir/bwt_test.cu.o [ 71%] Building CXX object nvBWT/CMakeFiles/nvBWT.dir/filelist.cpp.o [ 72%] Building CUDA object nvbio-test/CMakeFiles/nvbio-test.dir/condtion_test.cu.o [ 73%] Building CUDA object nvBowtie/CMakeFiles/nvBowtie.dir/bowtie2/cuda/aligner_best_approx_paired_wfa.cu.o [ 73%] Building CUDA object nvbio-test/CMakeFiles/nvbio-test.dir/cache_test.cu.o [ 74%] Building CUDA object nvbio-test/CMakeFiles/nvbio-test.dir/fmindex_test.cu.o [ 74%] Building CUDA object nvBowtie/CMakeFiles/nvBowtie.dir/bowtie2/cuda/aligner_init.cu.o [ 75%] Building CUDA object nvBowtie/CMakeFiles/nvBowtie.dir/bowtie2/cuda/aligner_best_approx_wfa.cu.o [ 76%] Building CUDA object nvBowtie/CMakeFiles/nvBowtie.dir/bowtie2/cuda/aligner_sort.cu.o [ 76%] Building CUDA object nvbio-test/CMakeFiles/nvbio-test.dir/fastq_test.cu.o [ 77%] Building CUDA object nvbio-test/CMakeFiles/nvbio-test.dir/rank_test.cu.o [ 78%] Building CUDA object nvbio-test/CMakeFiles/nvbio-test.dir/nvbio-test.cu.o [ 79%] Building CUDA object nvBowtie/CMakeFiles/nvBowtie.dir/bowtie2/cuda/compute_thread.cu.o [ 80%] Building CUDA object nvbio-test/CMakeFiles/nvbio-test.dir/sum_tree_test.cu.o [ 81%] Building CUDA object nvbio-test/CMakeFiles/nvbio-test.dir/syncblocks_test.cu.o [ 81%] Building CUDA object nvbio-test/CMakeFiles/nvbio-test.dir/string_set_test.cu.o [ 81%] Building CUDA object nvbio-test/CMakeFiles/nvbio-test.dir/packedstream_test.cu.o [ 81%] Building CUDA object nvBowtie/CMakeFiles/nvBowtie.dir/bowtie2/cuda/checksums.cu.o [ 82%] Building CUDA object nvbio-test/CMakeFiles/nvbio-test.dir/qgram_test.cu.o [ 84%] Building CUDA object nvBowtie/CMakeFiles/nvBowtie.dir/bowtie2/cuda/input_thread.cu.o [ 84%] Building CUDA object nvBowtie/CMakeFiles/nvBowtie.dir/bowtie2/cuda/mapping.cu.o [ 84%] Building CUDA object nvbio-test/CMakeFiles/nvbio-test.dir/work_queue_test.cu.o [ 83%] Building CUDA object nvBowtie/CMakeFiles/nvBowtie.dir/bowtie2/cuda/mapq.cu.o [ 84%] Building CUDA object nvBowtie/CMakeFiles/nvBowtie.dir/bowtie2/cuda/persist.cu.o [ 85%] Building CUDA object nvBowtie/CMakeFiles/nvBowtie.dir/bowtie2/cuda/params.cu.o [ 86%] Building CUDA object nvBowtie/CMakeFiles/nvBowtie.dir/bowtie2/cuda/output_thread.cu.o [ 87%] Building CUDA object nvBowtie/CMakeFiles/nvBowtie.dir/bowtie2/cuda/reduce.cu.o [ 88%] Building CUDA object nvBowtie/CMakeFiles/nvBowtie.dir/bowtie2/cuda/score_all.cu.o [ 89%] Building CUDA object nvbio-test/CMakeFiles/nvbio-test.dir/wavelet_test.cu.o [ 89%] Building CUDA object nvBowtie/CMakeFiles/nvBowtie.dir/bowtie2/cuda/score_best.cu.o [ 91%] Building CUDA object nvbio-test/CMakeFiles/nvbio-test.dir/sequence_test.cu.o [ 90%] Building CUDA object nvBowtie/CMakeFiles/nvBowtie.dir/bowtie2/cuda/score_gapped.cu.o [ 92%] Building CUDA object nvBowtie/CMakeFiles/nvBowtie.dir/bowtie2/cuda/score_ungapped.cu.o [ 93%] Building CUDA object nvBowtie/CMakeFiles/nvBowtie.dir/bowtie2/cuda/seed_hit_deque_array_test.cu.o [ 93%] Building CUDA object nvBowtie/CMakeFiles/nvBowtie.dir/bowtie2/cuda/seed_hit_deque_array.cu.o [ 93%] Building CUDA object nvBowtie/CMakeFiles/nvBowtie.dir/bowtie2/cuda/score_paired.cu.o [ 94%] Building CUDA object nvBowtie/CMakeFiles/nvBowtie.dir/bowtie2/cuda/scoring_queues_test.cu.o [ 95%] Building CUDA object nvBowtie/CMakeFiles/nvBowtie.dir/bowtie2/cuda/select.cu.o [ 95%] Building CUDA object nvBowtie/CMakeFiles/nvBowtie.dir/bowtie2/cuda/traceback.cu.o [ 96%] Building CUDA object nvBowtie/CMakeFiles/nvBowtie.dir/bowtie2/cuda/stats.cu.o [ 96%] Linking CUDA device code CMakeFiles/nvBWT.dir/cmake_device_link.o [ 97%] Linking CXX executable nvBWT make[3]: Leaving directory '/home/biocbuild/bbs-3.21-bioc-gpu/meat/RbowtieCuda/src/nvbio/build' [ 97%] Built target nvBWT [ 97%] Linking CUDA device code CMakeFiles/nvbio-test.dir/cmake_device_link.o [ 98%] Linking CXX executable nvbio-test make[3]: Leaving directory '/home/biocbuild/bbs-3.21-bioc-gpu/meat/RbowtieCuda/src/nvbio/build' [ 98%] Built target nvbio-test [ 99%] Linking CUDA device code CMakeFiles/nvBowtie.dir/cmake_device_link.o [100%] Linking CXX executable nvBowtie make[3]: Leaving directory '/home/biocbuild/bbs-3.21-bioc-gpu/meat/RbowtieCuda/src/nvbio/build' [100%] Built target nvBowtie make[2]: Leaving directory '/home/biocbuild/bbs-3.21-bioc-gpu/meat/RbowtieCuda/src/nvbio/build' make[1]: Leaving directory '/home/biocbuild/bbs-3.21-bioc-gpu/meat/RbowtieCuda/src/nvbio/build' cd "../src/nvbio/build" && cp nvBWT/nvBWT ../../../inst cd "../src/nvbio/build" && cp nvBowtie/nvBowtie ../../../inst cd "../src/nvbio/build" && cp nvbio-test/nvbio-test ../../../inst ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (RbowtieCuda)
RbowtieCuda.Rcheck/tests/runTests.Rout
R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
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Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
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> BiocGenerics:::testPackage("RbowtieCuda")
RbowtieCuda is distributed under the BSD 3-Clause License.
Please read the LICENSE file carefully before use.
Note:
- Redistribution and use (source/binary, with/without modification) are permitted
under certain conditions.
- The name of NVIDIA CORPORATION and its contributors may not be used to endorse
or promote derived products without written permission.
- This software is provided "AS IS", without warranty of any kind.
[22;32mverbose : cuda devices : 1
[22;32mverbose : device 0 has compute capability 8.0
[22;32mverbose : SM count : 108
[22;32mverbose : SM clock rate : 1410 Mhz
[22;32mverbose : memory clock rate : 1.2 Ghz
[22;32mverbose : chosen device 0
[22;32mverbose : device name : GRID A100X-10C
[22;32mverbose : compute capability : 8.0
[22;37minfo : alloc test... started
[22;37minfo : 1 MB:
[22;37minfo : cuda malloc : 0.33 ms, 2.980 GB/s
[22;37minfo : cuda free : 0.34 ms, 2.839 GB/s
[22;37minfo : malloc : 0.00 ms, 976.562 GB/s
[22;37minfo : free : 0.00 ms, 15625.000 GB/s
[22;37minfo : 4 MB:
[22;37minfo : cuda malloc : 0.32 ms, 12.088 GB/s
[22;37minfo : cuda free : 0.34 ms, 11.637 GB/s
[22;37minfo : malloc : 0.00 ms, 5000.000 GB/s
[22;37minfo : free : 0.00 ms, 8333.333 GB/s
[22;37minfo : 16 MB:
[22;37minfo : cuda malloc : 0.36 ms, 43.837 GB/s
[22;37minfo : cuda free : 0.38 ms, 40.677 GB/s
[22;37minfo : malloc : 0.00 ms, 17241.377 GB/s
[22;37minfo : free : 0.00 ms, 41666.660 GB/s
[22;37minfo : 64 MB:
[22;37minfo : cuda malloc : 0.37 ms, 170.445 GB/s
[22;37minfo : cuda free : 0.39 ms, 159.401 GB/s
[22;37minfo : malloc : 0.01 ms, 6734.006 GB/s
[22;37minfo : free : 0.01 ms, 6644.517 GB/s
[22;37minfo : 256 MB:
[22;37minfo : cuda malloc : 0.40 ms, 624.756 GB/s
[22;37minfo : cuda free : 0.49 ms, 505.274 GB/s
[22;37minfo : malloc : 0.01 ms, 26490.064 GB/s
[22;37minfo : free : 0.01 ms, 24096.391 GB/s
[22;37minfo : 1024 MB:
[22;37minfo : cuda malloc : 27.57 ms, 36.272 GB/s
[22;37minfo : cuda free : 0.92 ms, 1090.624 GB/s
[22;37minfo : malloc : 0.01 ms, 98461.539 GB/s
[22;37minfo : free : 0.02 ms, 46511.613 GB/s
[22;37minfo : alloc test... done
[01;31merror : caught a std::runtime_error exception:
[01;31merror : parallel_for failed: cudaErrorUnsupportedPtxVersion: the provided PTX was compiled with an unsupported toolchain.
RUNIT TEST PROTOCOL -- Wed Apr 9 14:19:05 2025
***********************************************
Number of test functions: 1
Number of errors: 0
Number of failures: 0
1 Test Suite :
RbowtieCuda RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
0.588 0.465 1.885
RbowtieCuda.Rcheck/RbowtieCuda-Ex.timings
| name | user | system | elapsed | |
| dot-callbinary2 | 0.000 | 0.005 | 0.005 | |
| nvBWT | 0.118 | 0.252 | 0.372 | |
| nvBowtie | 0.120 | 0.278 | 0.399 | |
| nvBowtie_usage | 0.002 | 0.001 | 0.004 | |
| nvBowtie_version | 0.002 | 0.002 | 0.005 | |
| nvbio_tests | 0.386 | 0.452 | 1.706 | |