Installation problems

[francicco]

Hi,

I'm reinstalling cactus due to conflict in the environment. I recompiled the kyoto libraries. Now what I did was

git clone https://github.com/ComparativeGenomicsToolkit/cactus.git
cd cactus
cd submodules && ln -s /mnt/storage/scratch/tk19812/software/clapack/ clapack (recompiled) && cd ..
virtualenv cactus_env
source cactus_env/bin/activate
pip install biopython boto3 coveralls cython deap ete3 gffutils graphviz matplotlib networkx numpy PyPDF2 pysam pytest pytest-cov PyYAML scipy seaborn 
pip install --upgrade toil

here I got this error:

Collecting actualSonLib (from progressiveCactus==1.0)
  ERROR: Could not find a version that satisfies the requirement actualSonLib (from progressiveCactus==1.0) (from versions: none)
ERROR: No matching distribution found for actualSonLib (from progressiveCactus==1.0)

then I did:

git submodule update --init
make
Building dependency sonLib
Building dependency pinchesAndCacti
Building dependency matchingAndOrdering
Building dependency cPecan
Building dependency hdf5
Building dependency hal

During hal I get this error:

inc/halPhyloP.h:16:24: fatal error: tree_model.h: No such file or directory

How should I fix this? Thanks a lot F

[francicco]

Maybe on google drive... need to make some space. Keep in mind that I used the same data previously (on the Cambridge cluster, it means some previous cactus version) and it was working.

F

[francicco]

This is the link Let me know if it works. F

[diekhans]

No, it want's me to login.

Do you have a public http or ftp server you can use? That is the way we normally share data.

Francesco Cicconardi notifications@github.com writes:

This is the link Let me know if it works. F

-- You are receiving this because you were mentioned. Reply to this email directly or view it on GitHub: https://github.com/ComparativeGenomicsToolkit/cactus/issues/103#issuecomment-596099349 This is the link Let me know if it works. F

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or unsubscribe.*

[francicco]

send me an email, it should work (francicco@gmail.com)

[francicco]

Hi @diekhans,

apparently the error is in line 35 of multiCactusProject.py. Specifically this: cactusPathElemList = xmlRoot.findall("cactus")

the list cactusPathElemList is empty. I don't know what xmlRoot.findall("cactus") suppose to do. But it basically the xml tree file is not generated.

F

[diekhans]

How long has does it take to fail?

[francicco]

real 0m23.403s user 0m0.999s sys 0m0.642s

[diekhans]

I have been running for 1.5 hours on a 64-core machine in single mode with no failure.

This is using single machine mode with local binaries, not Docker.

I would have left it running, except one of the genomes you send is older than the earlier configuration file Talp.v1.0.assembly.fasta vs Talp.v2.0.assembly.fasta

Are you sure the xml configuration files match what is checked into the tree?

Francesco Cicconardi notifications@github.com writes:

real 0m23.403s user 0m0.999s sys 0m0.642s

-- You are receiving this because you were mentioned. Reply to this email directly or view it on GitHub: https://github.com/ComparativeGenomicsToolkit/cactus/issues/103#issuecomment-597113549 real 0m23.403s user 0m0.999s sys 0m0.642s

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[francicco]

Did you use the conf file that I send you? F

[diekhans]

yes, excepted I changed it to reference the genomes you sent.

Francesco Cicconardi notifications@github.com writes:

Did you use the conf file that I send you? F

-- You are receiving this because you were mentioned. Reply to this email directly or view it on GitHub: https://github.com/ComparativeGenomicsToolkit/cactus/issues/103#issuecomment-597227733 Did you use the conf file that I send you? F

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[francicco]

can I see it? Maybe the error is there F

[francicco]

If I remove the --root flat it works F

[diekhans]

Can you send me the command line you are using?

Francesco Cicconardi notifications@github.com writes:

If I remove the --root flat it works F

-- You are receiving this because you were mentioned. Reply to this email directly or view it on GitHub: https://github.com/ComparativeGenomicsToolkit/cactus/issues/103#issuecomment-597236680 If I remove the --root flat it works F

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[francicco]

cactus /tmp/jobStore $OUTDIR/$CONFIG.conf $OUTDIR/$CONFIG.hal --binariesMode local --stats --logFile $OUTDIR/$CONFIG.log --maxCores $THREADS --defaultMemory $MEM --root Veme

[diekhans]

I can reproduce the failure now :-)

Francesco Cicconardi notifications@github.com writes:

cactus /tmp/jobStore $OUTDIR/$CONFIG.conf $OUTDIR/$CONFIG.hal --binariesMode local --stats --logFile $OUTDIR/$CONFIG.log --maxCores $THREADS --defaultMemory $MEM --root Veme

-- You are receiving this because you were mentioned. Reply to this email directly or view it on GitHub: https://github.com/ComparativeGenomicsToolkit/cactus/issues/103#issuecomment-597293543 cactus /tmp/jobStore $OUTDIR/$CONFIG.conf $OUTDIR/$CONFIG.hal --binariesMode local --stats --logFile $OUTDIR/$CONFIG.log --maxCores $THREADS --defaultMemory $MEM --root Veme

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[francicco]

Geez! I was feeling so stupid! HAHAHA F

[diekhans]

the root causes are:

• cactus doing a poor job of detected bad --root specified, a PR has been created that will give better error message
• you are specifying a root node that is actually a leaf in your tree, hence there is nothing to align. Why was this root selected? I am not sure you really need to specify a root.

[francicco]

I thought I need to specify the root of the tree, I can totally do it without. In case, should it be an internal branch? shell I use this syntax (((A,B)NODE_2,C)NODE_1,D); or something like this? (((A,B)[&&NHX:label=node_2],C)[&&NHX:label=node_1],D)[&&NHX:label=node_0];

thanks F

[diekhans]

Do you have particular genomes you want to use an outgroup? If so can use root to specify substree you wish to align the ones above it can be uses as outgroups. Otherwise, don't specify -root and it will default to the top of the tree

See examples/evolverMammals.txt for how to name an internal root.

Francesco Cicconardi notifications@github.com writes:

I thought I need to specify the root of the tree, I can totally do it without. In case, should it be an internal branch? shell I use this syntax (((A,B)NODE_2,C)NODE_1,D); or something like this? (((A,B)[&&NHX:label=node_2],C)[&&NHX:label=node_1],D)[&&NHX:label=node_0];

thanks F

-- You are receiving this because you were mentioned. Reply to this email directly or view it on GitHub: https://github.com/ComparativeGenomicsToolkit/cactus/issues/103#issuecomment-597519605 I thought I need to specify the root of the tree, I can totally do it without. In case, should it be an internal branch? shell I use this syntax (((A,B)NODE_2,C)NODE_1,D); or something like this? (((A,B)[&&NHX:label=node_2],C)[&&NHX:label=node_1],D)[&&NHX:label=node_0];

thanks F

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[francicco]

Cool! Thanks a lot F

[francicco]

Hi Mark,

I'm trying to reinstall cactus, given you updates. But I'm having problems again:

#================================================================
# Ready to install.
#================================================================
make[3]: Leaving directory `/mnt/storage/scratch/tk19812/software/cactus/submodules/kyoto/kyotocabinet'
grep -q '^CPPFLAGS.*-D_KCDEBUG' kyotocabinet/Makefile || make -j4 -C kyotocabinet strip
make[3]: Entering directory `/mnt/storage/scratch/tk19812/software/cactus/submodules/kyoto/kyotocabinet'
make[3]: warning: -jN forced in submake: disabling jobserver mode.
strip kcutiltest kcutilmgr kcprototest kcstashtest kccachetest kcgrasstest kchashtest kchashmgr kctreetest kctreemgr kcdirtest kcdirmgr kcforesttest kcforestmgr kcpolytest kcpolymgr kclangctest
make[3]: Leaving directory `/mnt/storage/scratch/tk19812/software/cactus/submodules/kyoto/kyotocabinet'
make -j4 -C kyototycoon
make[3]: Entering directory `/mnt/storage/scratch/tk19812/software/cactus/submodules/kyoto/kyototycoon'
make[3]: warning: -jN forced in submake: disabling jobserver mode.
g++ -g -O2 -Wall -fPIC -fsigned-char -g0 -O2 -Wno-unused-but-set-variable -Wno-unused-but-set-parameter -o ktutiltest ktutiltest.o -L../kyotocabinet -L/mnt/storage/home/tk19812/scratch/software/lzo-2.10/lib -L. -L/mnt/storage/home/tk19812/scratch/software/cactus/lib -L/usr/local/lib -L/mnt/storage/home/tk19812/scratch/software/cactus/lib -Lno/lib -Wl,-rpath-link,.:/usr/local/lib:.:/usr/local/lib:/mnt/storage/easybuild/software/HDF5/1.8.17-foss-2016b/lib:/mnt/storage/easybuild/software/Szip/2.1-foss-2016b/lib:/mnt/storage/easybuild/software/zlib/1.2.8-foss-2016b/lib:/mnt/storage/easybuild/software/ScaLAPACK/2.0.2-gompi-2016b-OpenBLAS-0.2.18-LAPACK-3.6.1/lib:/mnt/storage/easybuild/software/OpenBLAS/0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.1/lib:/mnt/storage/easybuild/software/FFTW/3.3.4-gompi-2016b/lib:/mnt/storage/easybuild/software/OpenMPI/1.10.3-GCC-5.4.0-2.26/lib:/mnt/storage/easybuild/software/hwloc/1.11.3-GCC-5.4.0-2.26/lib:/mnt/storage/easybuild/software/numactl/2.0.11-GCC-5.4.0-2.26/lib:/mnt/storage/easybuild/software/binutils/2.26-GCCcore-5.4.0/lib:/mnt/storage/easybuild/software/GCCcore/5.4.0/lib/gcc/x86_64-unknown-linux-gnu/5.4.0:/mnt/storage/easybuild/software/GCCcore/5.4.0/lib64:/mnt/storage/easybuild/software/GCCcore/5.4.0/lib:/mnt/storage/software/apps/ncbi-blast/gnu/2.7.1/lib:/mnt/storage/easybuild/software/R/3.2.3-foss-2016a/lib64/R/lib:/mnt/storage/easybuild/software/R/3.2.3-foss-2016a/lib64:/mnt/storage/easybuild/software/GMP/6.1.0-foss-2016a/lib:/mnt/storage/easybuild/software/PROJ/4.9.2-foss-2016a/lib:/mnt/storage/easybuild/software/GDAL/2.0.2-foss-2016a/lib:/mnt/storage/easybuild/software/expat/2.1.0-foss-2016a/lib:/mnt/storage/easybuild/software/netCDF/4.3.3.1-foss-2016a/lib64:/mnt/storage/easybuild/software/libxml2/2.9.3-foss-2016a/lib:/mnt/storage/easybuild/software/cURL/7.47.0-foss-2016a/lib:/mnt/storage/easybuild/software/Tk/8.6.4-foss-2016a-no-X11/lib:/mnt/storage/easybuild/software/Tcl/8.6.4-foss-2016a/lib:/mnt/storage/easybuild/software/Java/1.8.0_72/lib:/mnt/storage/easybuild/software/libjpeg-turbo/1.4.2-foss-2016a/lib:/mnt/storage/easybuild/software/libpng/1.6.21-foss-2016a/lib:/mnt/storage/easybuild/software/libreadline/6.3-foss-2016a/lib:/mnt/storage/easybuild/software/ncurses/6.0-foss-2016a/lib:/mnt/storage/easybuild/software/bzip2/1.0.6-foss-2016a/lib:/mnt/storage/easybuild/software/GSL/2.3-foss-2017a/lib:/mnt/storage/easybuild/software/SQLite/3.13.0-GCC-5.4.0-2.26/lib:/mnt/storage/home/tk19812/software/lpsolve-5.5.0.10i/lib:/mnt/storage/home/tk19812/scratch/software/sparsehash/include:/mnt/storage/home/tk19812/scratch/software/bamtools/usr/local/lib64:/mnt/storage/home/tk19812/scratch/software/lzo-2.10/lib:/mnt/storage/home/tk19812/scratch/software/WiggleTools/lib:/mnt/storage/home/tk19812/scratch/software/cactus/lua-5.1.5/lib:/mnt/storage/home/tk19812/scratch/software/lzo-2.10/lib:/mnt/storage/home/tk19812/scratch/software/kyoto/lib:/mnt/storage/home/tk19812/scratch/software/swig-4.0.1/Lib:/mnt/storage/home/tk19812/scratch/software/openssl-1.1.1d/lib:/mnt/storage/home/tk19812/scratch/software/libBigWig/lib:/mnt/storage/home/tk19812/scratch/software/SuiteSparse/lib:/mnt/storage/home/tk19812/scratch/software/libuv-v1.37.0/.libs:/mnt/storage/home/tk19812/scratch/software/nghttp2-1.40.0/lib/.libs:/mnt/storage/home/tk19812/scratch/software/openldap/libraries/liblmdb:/mnt/storage/home/tk19812/scratch/CIRCOS/circos-0.69-9/libgd-2.3.0/lib:/mnt/storage/home/tk19812/scratch/software/jemalloc/lib:/mnt/storage/home/tk19812/.conda/envs/test3k/lib:/mnt/storage/home/tk19812/scratch/software/portcullis/lib/python3.7/site-packages:/mnt/storage/home/tk19812/scratch/software/portcullis/boost_1_67_0/stage/lib:/mnt/storage/home/tk19812/scratch/software/cactus/lib:no/lib -Wl,--as-needed -static -L../kyotocabinet -L/mnt/storage/home/tk19812/scratch/software/lzo-2.10/lib -L. -L/mnt/storage/home/tk19812/scratch/software/cactus/lib -L/usr/local/lib -L/mnt/storage/home/tk19812/scratch/software/cactus/lib -Lno/lib -Wl,-rpath-link,.:/usr/local/lib:.:/usr/local/lib:/mnt/storage/easybuild/software/HDF5/1.8.17-foss-2016b/lib:/mnt/storage/easybuild/software/Szip/2.1-foss-2016b/lib:/mnt/storage/easybuild/software/zlib/1.2.8-foss-2016b/lib:/mnt/storage/easybuild/software/ScaLAPACK/2.0.2-gompi-2016b-OpenBLAS-0.2.18-LAPACK-3.6.1/lib:/mnt/storage/easybuild/software/OpenBLAS/0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.1/lib:/mnt/storage/easybuild/software/FFTW/3.3.4-gompi-2016b/lib:/mnt/storage/easybuild/software/OpenMPI/1.10.3-GCC-5.4.0-2.26/lib:/mnt/storage/easybuild/software/hwloc/1.11.3-GCC-5.4.0-2.26/lib:/mnt/storage/easybuild/software/numactl/2.0.11-GCC-5.4.0-2.26/lib:/mnt/storage/easybuild/software/binutils/2.26-GCCcore-5.4.0/lib:/mnt/storage/easybuild/software/GCCcore/5.4.0/lib/gcc/x86_64-unknown-linux-gnu/5.4.0:/mnt/storage/easybuild/software/GCCcore/5.4.0/lib64:/mnt/storage/easybuild/software/GCCcore/5.4.0/lib:/mnt/storage/software/apps/ncbi-blast/gnu/2.7.1/lib:/mnt/storage/easybuild/software/R/3.2.3-foss-2016a/lib64/R/lib:/mnt/storage/easybuild/software/R/3.2.3-foss-2016a/lib64:/mnt/storage/easybuild/software/GMP/6.1.0-foss-2016a/lib:/mnt/storage/easybuild/software/PROJ/4.9.2-foss-2016a/lib:/mnt/storage/easybuild/software/GDAL/2.0.2-foss-2016a/lib:/mnt/storage/easybuild/software/expat/2.1.0-foss-2016a/lib:/mnt/storage/easybuild/software/netCDF/4.3.3.1-foss-2016a/lib64:/mnt/storage/easybuild/software/libxml2/2.9.3-foss-2016a/lib:/mnt/storage/easybuild/software/cURL/7.47.0-foss-2016a/lib:/mnt/storage/easybuild/software/Tk/8.6.4-foss-2016a-no-X11/lib:/mnt/storage/easybuild/software/Tcl/8.6.4-foss-2016a/lib:/mnt/storage/easybuild/software/Java/1.8.0_72/lib:/mnt/storage/easybuild/software/libjpeg-turbo/1.4.2-foss-2016a/lib:/mnt/storage/easybuild/software/libpng/1.6.21-foss-2016a/lib:/mnt/storage/easybuild/software/libreadline/6.3-foss-2016a/lib:/mnt/storage/easybuild/software/ncurses/6.0-foss-2016a/lib:/mnt/storage/easybuild/software/bzip2/1.0.6-foss-2016a/lib:/mnt/storage/easybuild/software/GSL/2.3-foss-2017a/lib:/mnt/storage/easybuild/software/SQLite/3.13.0-GCC-5.4.0-2.26/lib:/mnt/storage/home/tk19812/software/lpsolve-5.5.0.10i/lib:/mnt/storage/home/tk19812/scratch/software/sparsehash/include:/mnt/storage/home/tk19812/scratch/software/bamtools/usr/local/lib64:/mnt/storage/home/tk19812/scratch/software/lzo-2.10/lib:/mnt/storage/home/tk19812/scratch/software/WiggleTools/lib:/mnt/storage/home/tk19812/scratch/software/cactus/lua-5.1.5/lib:/mnt/storage/home/tk19812/scratch/software/lzo-2.10/lib:/mnt/storage/home/tk19812/scratch/software/kyoto/lib:/mnt/storage/home/tk19812/scratch/software/swig-4.0.1/Lib:/mnt/storage/home/tk19812/scratch/software/openssl-1.1.1d/lib:/mnt/storage/home/tk19812/scratch/software/libBigWig/lib:/mnt/storage/home/tk19812/scratch/software/SuiteSparse/lib:/mnt/storage/home/tk19812/scratch/software/libuv-v1.37.0/.libs:/mnt/storage/home/tk19812/scratch/software/nghttp2-1.40.0/lib/.libs:/mnt/storage/home/tk19812/scratch/software/openldap/libraries/liblmdb:/mnt/storage/home/tk19812/scratch/CIRCOS/circos-0.69-9/libgd-2.3.0/lib:/mnt/storage/home/tk19812/scratch/software/jemalloc/lib:/mnt/storage/home/tk19812/.conda/envs/test3k/lib:/mnt/storage/home/tk19812/scratch/software/portcullis/lib/python3.7/site-packages:/mnt/storage/home/tk19812/scratch/software/portcullis/boost_1_67_0/stage/lib:/mnt/storage/home/tk19812/scratch/software/cactus/lib:no/lib -Wl,--as-needed -lkyototycoon -lkyotocabinet -lkyotocabinet -llzma -llzo2 -lz -lstdc++ -lresolv -lnsl -ldl -lrt -lpthread -lm -lc  -lkyotocabinet -llzma -llzo2 -lz -lstdc++ -lresolv -lnsl -ldl -lrt -lpthread -lm -lc 
g++ -g -O2 -Wall -fPIC -fsigned-char -g0 -O2 -Wno-unused-but-set-variable -Wno-unused-but-set-parameter -o ktutilmgr ktutilmgr.o -L../kyotocabinet -L/mnt/storage/home/tk19812/scratch/software/lzo-2.10/lib -L. -L/mnt/storage/home/tk19812/scratch/software/cactus/lib -L/usr/local/lib -L/mnt/storage/home/tk19812/scratch/software/cactus/lib -Lno/lib -Wl,-rpath-link,.:/usr/local/lib:.:/usr/local/lib:/mnt/storage/easybuild/software/HDF5/1.8.17-foss-2016b/lib:/mnt/storage/easybuild/software/Szip/2.1-foss-2016b/lib:/mnt/storage/easybuild/software/zlib/1.2.8-foss-2016b/lib:/mnt/storage/easybuild/software/ScaLAPACK/2.0.2-gompi-2016b-OpenBLAS-0.2.18-LAPACK-3.6.1/lib:/mnt/storage/easybuild/software/OpenBLAS/0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.1/lib:/mnt/storage/easybuild/software/FFTW/3.3.4-gompi-2016b/lib:/mnt/storage/easybuild/software/OpenMPI/1.10.3-GCC-5.4.0-2.26/lib:/mnt/storage/easybuild/software/hwloc/1.11.3-GCC-5.4.0-2.26/lib:/mnt/storage/easybuild/software/numactl/2.0.11-GCC-5.4.0-2.26/lib:/mnt/storage/easybuild/software/binutils/2.26-GCCcore-5.4.0/lib:/mnt/storage/easybuild/software/GCCcore/5.4.0/lib/gcc/x86_64-unknown-linux-gnu/5.4.0:/mnt/storage/easybuild/software/GCCcore/5.4.0/lib64:/mnt/storage/easybuild/software/GCCcore/5.4.0/lib:/mnt/storage/software/apps/ncbi-blast/gnu/2.7.1/lib:/mnt/storage/easybuild/software/R/3.2.3-foss-2016a/lib64/R/lib:/mnt/storage/easybuild/software/R/3.2.3-foss-2016a/lib64:/mnt/storage/easybuild/software/GMP/6.1.0-foss-2016a/lib:/mnt/storage/easybuild/software/PROJ/4.9.2-foss-2016a/lib:/mnt/storage/easybuild/software/GDAL/2.0.2-foss-2016a/lib:/mnt/storage/easybuild/software/expat/2.1.0-foss-2016a/lib:/mnt/storage/easybuild/software/netCDF/4.3.3.1-foss-2016a/lib64:/mnt/storage/easybuild/software/libxml2/2.9.3-foss-2016a/lib:/mnt/storage/easybuild/software/cURL/7.47.0-foss-2016a/lib:/mnt/storage/easybuild/software/Tk/8.6.4-foss-2016a-no-X11/lib:/mnt/storage/easybuild/software/Tcl/8.6.4-foss-2016a/lib:/mnt/storage/easybuild/software/Java/1.8.0_72/lib:/mnt/storage/easybuild/software/libjpeg-turbo/1.4.2-foss-2016a/lib:/mnt/storage/easybuild/software/libpng/1.6.21-foss-2016a/lib:/mnt/storage/easybuild/software/libreadline/6.3-foss-2016a/lib:/mnt/storage/easybuild/software/ncurses/6.0-foss-2016a/lib:/mnt/storage/easybuild/software/bzip2/1.0.6-foss-2016a/lib:/mnt/storage/easybuild/software/GSL/2.3-foss-2017a/lib:/mnt/storage/easybuild/software/SQLite/3.13.0-GCC-5.4.0-2.26/lib:/mnt/storage/home/tk19812/software/lpsolve-5.5.0.10i/lib:/mnt/storage/home/tk19812/scratch/software/sparsehash/include:/mnt/storage/home/tk19812/scratch/software/bamtools/usr/local/lib64:/mnt/storage/home/tk19812/scratch/software/lzo-2.10/lib:/mnt/storage/home/tk19812/scratch/software/WiggleTools/lib:/mnt/storage/home/tk19812/scratch/software/cactus/lua-5.1.5/lib:/mnt/storage/home/tk19812/scratch/software/lzo-2.10/lib:/mnt/storage/home/tk19812/scratch/software/kyoto/lib:/mnt/storage/home/tk19812/scratch/software/swig-4.0.1/Lib:/mnt/storage/home/tk19812/scratch/software/openssl-1.1.1d/lib:/mnt/storage/home/tk19812/scratch/software/libBigWig/lib:/mnt/storage/home/tk19812/scratch/software/SuiteSparse/lib:/mnt/storage/home/tk19812/scratch/software/libuv-v1.37.0/.libs:/mnt/storage/home/tk19812/scratch/software/nghttp2-1.40.0/lib/.libs:/mnt/storage/home/tk19812/scratch/software/openldap/libraries/liblmdb:/mnt/storage/home/tk19812/scratch/CIRCOS/circos-0.69-9/libgd-2.3.0/lib:/mnt/storage/home/tk19812/scratch/software/jemalloc/lib:/mnt/storage/home/tk19812/.conda/envs/test3k/lib:/mnt/storage/home/tk19812/scratch/software/portcullis/lib/python3.7/site-packages:/mnt/storage/home/tk19812/scratch/software/portcullis/boost_1_67_0/stage/lib:/mnt/storage/home/tk19812/scratch/software/cactus/lib:no/lib -Wl,--as-needed -static -L../kyotocabinet -L/mnt/storage/home/tk19812/scratch/software/lzo-2.10/lib -L. -L/mnt/storage/home/tk19812/scratch/software/cactus/lib -L/usr/local/lib -L/mnt/storage/home/tk19812/scratch/software/cactus/lib -Lno/lib -Wl,-rpath-link,.:/usr/local/lib:.:/usr/local/lib:/mnt/storage/easybuild/software/HDF5/1.8.17-foss-2016b/lib:/mnt/storage/easybuild/software/Szip/2.1-foss-2016b/lib:/mnt/storage/easybuild/software/zlib/1.2.8-foss-2016b/lib:/mnt/storage/easybuild/software/ScaLAPACK/2.0.2-gompi-2016b-OpenBLAS-0.2.18-LAPACK-3.6.1/lib:/mnt/storage/easybuild/software/OpenBLAS/0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.1/lib:/mnt/storage/easybuild/software/FFTW/3.3.4-gompi-2016b/lib:/mnt/storage/easybuild/software/OpenMPI/1.10.3-GCC-5.4.0-2.26/lib:/mnt/storage/easybuild/software/hwloc/1.11.3-GCC-5.4.0-2.26/lib:/mnt/storage/easybuild/software/numactl/2.0.11-GCC-5.4.0-2.26/lib:/mnt/storage/easybuild/software/binutils/2.26-GCCcore-5.4.0/lib:/mnt/storage/easybuild/software/GCCcore/5.4.0/lib/gcc/x86_64-unknown-linux-gnu/5.4.0:/mnt/storage/easybuild/software/GCCcore/5.4.0/lib64:/mnt/storage/easybuild/software/GCCcore/5.4.0/lib:/mnt/storage/software/apps/ncbi-blast/gnu/2.7.1/lib:/mnt/storage/easybuild/software/R/3.2.3-foss-2016a/lib64/R/lib:/mnt/storage/easybuild/software/R/3.2.3-foss-2016a/lib64:/mnt/storage/easybuild/software/GMP/6.1.0-foss-2016a/lib:/mnt/storage/easybuild/software/PROJ/4.9.2-foss-2016a/lib:/mnt/storage/easybuild/software/GDAL/2.0.2-foss-2016a/lib:/mnt/storage/easybuild/software/expat/2.1.0-foss-2016a/lib:/mnt/storage/easybuild/software/netCDF/4.3.3.1-foss-2016a/lib64:/mnt/storage/easybuild/software/libxml2/2.9.3-foss-2016a/lib:/mnt/storage/easybuild/software/cURL/7.47.0-foss-2016a/lib:/mnt/storage/easybuild/software/Tk/8.6.4-foss-2016a-no-X11/lib:/mnt/storage/easybuild/software/Tcl/8.6.4-foss-2016a/lib:/mnt/storage/easybuild/software/Java/1.8.0_72/lib:/mnt/storage/easybuild/software/libjpeg-turbo/1.4.2-foss-2016a/lib:/mnt/storage/easybuild/software/libpng/1.6.21-foss-2016a/lib:/mnt/storage/easybuild/software/libreadline/6.3-foss-2016a/lib:/mnt/storage/easybuild/software/ncurses/6.0-foss-2016a/lib:/mnt/storage/easybuild/software/bzip2/1.0.6-foss-2016a/lib:/mnt/storage/easybuild/software/GSL/2.3-foss-2017a/lib:/mnt/storage/easybuild/software/SQLite/3.13.0-GCC-5.4.0-2.26/lib:/mnt/storage/home/tk19812/software/lpsolve-5.5.0.10i/lib:/mnt/storage/home/tk19812/scratch/software/sparsehash/include:/mnt/storage/home/tk19812/scratch/software/bamtools/usr/local/lib64:/mnt/storage/home/tk19812/scratch/software/lzo-2.10/lib:/mnt/storage/home/tk19812/scratch/software/WiggleTools/lib:/mnt/storage/home/tk19812/scratch/software/cactus/lua-5.1.5/lib:/mnt/storage/home/tk19812/scratch/software/lzo-2.10/lib:/mnt/storage/home/tk19812/scratch/software/kyoto/lib:/mnt/storage/home/tk19812/scratch/software/swig-4.0.1/Lib:/mnt/storage/home/tk19812/scratch/software/openssl-1.1.1d/lib:/mnt/storage/home/tk19812/scratch/software/libBigWig/lib:/mnt/storage/home/tk19812/scratch/software/SuiteSparse/lib:/mnt/storage/home/tk19812/scratch/software/libuv-v1.37.0/.libs:/mnt/storage/home/tk19812/scratch/software/nghttp2-1.40.0/lib/.libs:/mnt/storage/home/tk19812/scratch/software/openldap/libraries/liblmdb:/mnt/storage/home/tk19812/scratch/CIRCOS/circos-0.69-9/libgd-2.3.0/lib:/mnt/storage/home/tk19812/scratch/software/jemalloc/lib:/mnt/storage/home/tk19812/.conda/envs/test3k/lib:/mnt/storage/home/tk19812/scratch/software/portcullis/lib/python3.7/site-packages:/mnt/storage/home/tk19812/scratch/software/portcullis/boost_1_67_0/stage/lib:/mnt/storage/home/tk19812/scratch/software/cactus/lib:no/lib -Wl,--as-needed -lkyototycoon -lkyotocabinet -lkyotocabinet -llzma -llzo2 -lz -lstdc++ -lresolv -lnsl -ldl -lrt -lpthread -lm -lc  -lkyotocabinet -llzma -llzo2 -lz -lstdc++ -lresolv -lnsl -ldl -lrt -lpthread -lm -lc 
g++ -g -O2 -Wall -fPIC -fsigned-char -g0 -O2 -Wno-unused-but-set-variable -Wno-unused-but-set-parameter -o ktutilserv ktutilserv.o -L../kyotocabinet -L/mnt/storage/home/tk19812/scratch/software/lzo-2.10/lib -L. -L/mnt/storage/home/tk19812/scratch/software/cactus/lib -L/usr/local/lib -L/mnt/storage/home/tk19812/scratch/software/cactus/lib -Lno/lib -Wl,-rpath-link,.:/usr/local/lib:.:/usr/local/lib:/mnt/storage/easybuild/software/HDF5/1.8.17-foss-2016b/lib:/mnt/storage/easybuild/software/Szip/2.1-foss-2016b/lib:/mnt/storage/easybuild/software/zlib/1.2.8-foss-2016b/lib:/mnt/storage/easybuild/software/ScaLAPACK/2.0.2-gompi-2016b-OpenBLAS-0.2.18-LAPACK-3.6.1/lib:/mnt/storage/easybuild/software/OpenBLAS/0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.1/lib:/mnt/storage/easybuild/software/FFTW/3.3.4-gompi-2016b/lib:/mnt/storage/easybuild/software/OpenMPI/1.10.3-GCC-5.4.0-2.26/lib:/mnt/storage/easybuild/software/hwloc/1.11.3-GCC-5.4.0-2.26/lib:/mnt/storage/easybuild/software/numactl/2.0.11-GCC-5.4.0-2.26/lib:/mnt/storage/easybuild/software/binutils/2.26-GCCcore-5.4.0/lib:/mnt/storage/easybuild/software/GCCcore/5.4.0/lib/gcc/x86_64-unknown-linux-gnu/5.4.0:/mnt/storage/easybuild/software/GCCcore/5.4.0/lib64:/mnt/storage/easybuild/software/GCCcore/5.4.0/lib:/mnt/storage/software/apps/ncbi-blast/gnu/2.7.1/lib:/mnt/storage/easybuild/software/R/3.2.3-foss-2016a/lib64/R/lib:/mnt/storage/easybuild/software/R/3.2.3-foss-2016a/lib64:/mnt/storage/easybuild/software/GMP/6.1.0-foss-2016a/lib:/mnt/storage/easybuild/software/PROJ/4.9.2-foss-2016a/lib:/mnt/storage/easybuild/software/GDAL/2.0.2-foss-2016a/lib:/mnt/storage/easybuild/software/expat/2.1.0-foss-2016a/lib:/mnt/storage/easybuild/software/netCDF/4.3.3.1-foss-2016a/lib64:/mnt/storage/easybuild/software/libxml2/2.9.3-foss-2016a/lib:/mnt/storage/easybuild/software/cURL/7.47.0-foss-2016a/lib:/mnt/storage/easybuild/software/Tk/8.6.4-foss-2016a-no-X11/lib:/mnt/storage/easybuild/software/Tcl/8.6.4-foss-2016a/lib:/mnt/storage/easybuild/software/Java/1.8.0_72/lib:/mnt/storage/easybuild/software/libjpeg-turbo/1.4.2-foss-2016a/lib:/mnt/storage/easybuild/software/libpng/1.6.21-foss-2016a/lib:/mnt/storage/easybuild/software/libreadline/6.3-foss-2016a/lib:/mnt/storage/easybuild/software/ncurses/6.0-foss-2016a/lib:/mnt/storage/easybuild/software/bzip2/1.0.6-foss-2016a/lib:/mnt/storage/easybuild/software/GSL/2.3-foss-2017a/lib:/mnt/storage/easybuild/software/SQLite/3.13.0-GCC-5.4.0-2.26/lib:/mnt/storage/home/tk19812/software/lpsolve-5.5.0.10i/lib:/mnt/storage/home/tk19812/scratch/software/sparsehash/include:/mnt/storage/home/tk19812/scratch/software/bamtools/usr/local/lib64:/mnt/storage/home/tk19812/scratch/software/lzo-2.10/lib:/mnt/storage/home/tk19812/scratch/software/WiggleTools/lib:/mnt/storage/home/tk19812/scratch/software/cactus/lua-5.1.5/lib:/mnt/storage/home/tk19812/scratch/software/lzo-2.10/lib:/mnt/storage/home/tk19812/scratch/software/kyoto/lib:/mnt/storage/home/tk19812/scratch/software/swig-4.0.1/Lib:/mnt/storage/home/tk19812/scratch/software/openssl-1.1.1d/lib:/mnt/storage/home/tk19812/scratch/software/libBigWig/lib:/mnt/storage/home/tk19812/scratch/software/SuiteSparse/lib:/mnt/storage/home/tk19812/scratch/software/libuv-v1.37.0/.libs:/mnt/storage/home/tk19812/scratch/software/nghttp2-1.40.0/lib/.libs:/mnt/storage/home/tk19812/scratch/software/openldap/libraries/liblmdb:/mnt/storage/home/tk19812/scratch/CIRCOS/circos-0.69-9/libgd-2.3.0/lib:/mnt/storage/home/tk19812/scratch/software/jemalloc/lib:/mnt/storage/home/tk19812/.conda/envs/test3k/lib:/mnt/storage/home/tk19812/scratch/software/portcullis/lib/python3.7/site-packages:/mnt/storage/home/tk19812/scratch/software/portcullis/boost_1_67_0/stage/lib:/mnt/storage/home/tk19812/scratch/software/cactus/lib:no/lib -Wl,--as-needed -static -L../kyotocabinet -L/mnt/storage/home/tk19812/scratch/software/lzo-2.10/lib -L. -L/mnt/storage/home/tk19812/scratch/software/cactus/lib -L/usr/local/lib -L/mnt/storage/home/tk19812/scratch/software/cactus/lib -Lno/lib -Wl,-rpath-link,.:/usr/local/lib:.:/usr/local/lib:/mnt/storage/easybuild/software/HDF5/1.8.17-foss-2016b/lib:/mnt/storage/easybuild/software/Szip/2.1-foss-2016b/lib:/mnt/storage/easybuild/software/zlib/1.2.8-foss-2016b/lib:/mnt/storage/easybuild/software/ScaLAPACK/2.0.2-gompi-2016b-OpenBLAS-0.2.18-LAPACK-3.6.1/lib:/mnt/storage/easybuild/software/OpenBLAS/0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.1/lib:/mnt/storage/easybuild/software/FFTW/3.3.4-gompi-2016b/lib:/mnt/storage/easybuild/software/OpenMPI/1.10.3-GCC-5.4.0-2.26/lib:/mnt/storage/easybuild/software/hwloc/1.11.3-GCC-5.4.0-2.26/lib:/mnt/storage/easybuild/software/numactl/2.0.11-GCC-5.4.0-2.26/lib:/mnt/storage/easybuild/software/binutils/2.26-GCCcore-5.4.0/lib:/mnt/storage/easybuild/software/GCCcore/5.4.0/lib/gcc/x86_64-unknown-linux-gnu/5.4.0:/mnt/storage/easybuild/software/GCCcore/5.4.0/lib64:/mnt/storage/easybuild/software/GCCcore/5.4.0/lib:/mnt/storage/software/apps/ncbi-blast/gnu/2.7.1/lib:/mnt/storage/easybuild/software/R/3.2.3-foss-2016a/lib64/R/lib:/mnt/storage/easybuild/software/R/3.2.3-foss-2016a/lib64:/mnt/storage/easybuild/software/GMP/6.1.0-foss-2016a/lib:/mnt/storage/easybuild/software/PROJ/4.9.2-foss-2016a/lib:/mnt/storage/easybuild/software/GDAL/2.0.2-foss-2016a/lib:/mnt/storage/easybuild/software/expat/2.1.0-foss-2016a/lib:/mnt/storage/easybuild/software/netCDF/4.3.3.1-foss-2016a/lib64:/mnt/storage/easybuild/software/libxml2/2.9.3-foss-2016a/lib:/mnt/storage/easybuild/software/cURL/7.47.0-foss-2016a/lib:/mnt/storage/easybuild/software/Tk/8.6.4-foss-2016a-no-X11/lib:/mnt/storage/easybuild/software/Tcl/8.6.4-foss-2016a/lib:/mnt/storage/easybuild/software/Java/1.8.0_72/lib:/mnt/storage/easybuild/software/libjpeg-turbo/1.4.2-foss-2016a/lib:/mnt/storage/easybuild/software/libpng/1.6.21-foss-2016a/lib:/mnt/storage/easybuild/software/libreadline/6.3-foss-2016a/lib:/mnt/storage/easybuild/software/ncurses/6.0-foss-2016a/lib:/mnt/storage/easybuild/software/bzip2/1.0.6-foss-2016a/lib:/mnt/storage/easybuild/software/GSL/2.3-foss-2017a/lib:/mnt/storage/easybuild/software/SQLite/3.13.0-GCC-5.4.0-2.26/lib:/mnt/storage/home/tk19812/software/lpsolve-5.5.0.10i/lib:/mnt/storage/home/tk19812/scratch/software/sparsehash/include:/mnt/storage/home/tk19812/scratch/software/bamtools/usr/local/lib64:/mnt/storage/home/tk19812/scratch/software/lzo-2.10/lib:/mnt/storage/home/tk19812/scratch/software/WiggleTools/lib:/mnt/storage/home/tk19812/scratch/software/cactus/lua-5.1.5/lib:/mnt/storage/home/tk19812/scratch/software/lzo-2.10/lib:/mnt/storage/home/tk19812/scratch/software/kyoto/lib:/mnt/storage/home/tk19812/scratch/software/swig-4.0.1/Lib:/mnt/storage/home/tk19812/scratch/software/openssl-1.1.1d/lib:/mnt/storage/home/tk19812/scratch/software/libBigWig/lib:/mnt/storage/home/tk19812/scratch/software/SuiteSparse/lib:/mnt/storage/home/tk19812/scratch/software/libuv-v1.37.0/.libs:/mnt/storage/home/tk19812/scratch/software/nghttp2-1.40.0/lib/.libs:/mnt/storage/home/tk19812/scratch/software/openldap/libraries/liblmdb:/mnt/storage/home/tk19812/scratch/CIRCOS/circos-0.69-9/libgd-2.3.0/lib:/mnt/storage/home/tk19812/scratch/software/jemalloc/lib:/mnt/storage/home/tk19812/.conda/envs/test3k/lib:/mnt/storage/home/tk19812/scratch/software/portcullis/lib/python3.7/site-packages:/mnt/storage/home/tk19812/scratch/software/portcullis/boost_1_67_0/stage/lib:/mnt/storage/home/tk19812/scratch/software/cactus/lib:no/lib -Wl,--as-needed -lkyototycoon -lkyotocabinet -lkyotocabinet -llzma -llzo2 -lz -lstdc++ -lresolv -lnsl -ldl -lrt -lpthread -lm -lc  -lkyotocabinet -llzma -llzo2 -lz -lstdc++ -lresolv -lnsl -ldl -lrt -lpthread -lm -lc 
g++ -g -O2 -Wall -fPIC -fsigned-char -g0 -O2 -Wno-unused-but-set-variable -Wno-unused-but-set-parameter -o kttimedtest kttimedtest.o -L../kyotocabinet -L/mnt/storage/home/tk19812/scratch/software/lzo-2.10/lib -L. -L/mnt/storage/home/tk19812/scratch/software/cactus/lib -L/usr/local/lib -L/mnt/storage/home/tk19812/scratch/software/cactus/lib -Lno/lib -Wl,-rpath-link,.:/usr/local/lib:.:/usr/local/lib:/mnt/storage/easybuild/software/HDF5/1.8.17-foss-2016b/lib:/mnt/storage/easybuild/software/Szip/2.1-foss-2016b/lib:/mnt/storage/easybuild/software/zlib/1.2.8-foss-2016b/lib:/mnt/storage/easybuild/software/ScaLAPACK/2.0.2-gompi-2016b-OpenBLAS-0.2.18-LAPACK-3.6.1/lib:/mnt/storage/easybuild/software/OpenBLAS/0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.1/lib:/mnt/storage/easybuild/software/FFTW/3.3.4-gompi-2016b/lib:/mnt/storage/easybuild/software/OpenMPI/1.10.3-GCC-5.4.0-2.26/lib:/mnt/storage/easybuild/software/hwloc/1.11.3-GCC-5.4.0-2.26/lib:/mnt/storage/easybuild/software/numactl/2.0.11-GCC-5.4.0-2.26/lib:/mnt/storage/easybuild/software/binutils/2.26-GCCcore-5.4.0/lib:/mnt/storage/easybuild/software/GCCcore/5.4.0/lib/gcc/x86_64-unknown-linux-gnu/5.4.0:/mnt/storage/easybuild/software/GCCcore/5.4.0/lib64:/mnt/storage/easybuild/software/GCCcore/5.4.0/lib:/mnt/storage/software/apps/ncbi-blast/gnu/2.7.1/lib:/mnt/storage/easybuild/software/R/3.2.3-foss-2016a/lib64/R/lib:/mnt/storage/easybuild/software/R/3.2.3-foss-2016a/lib64:/mnt/storage/easybuild/software/GMP/6.1.0-foss-2016a/lib:/mnt/storage/easybuild/software/PROJ/4.9.2-foss-2016a/lib:/mnt/storage/easybuild/software/GDAL/2.0.2-foss-2016a/lib:/mnt/storage/easybuild/software/expat/2.1.0-foss-2016a/lib:/mnt/storage/easybuild/software/netCDF/4.3.3.1-foss-2016a/lib64:/mnt/storage/easybuild/software/libxml2/2.9.3-foss-2016a/lib:/mnt/storage/easybuild/software/cURL/7.47.0-foss-2016a/lib:/mnt/storage/easybuild/software/Tk/8.6.4-foss-2016a-no-X11/lib:/mnt/storage/easybuild/software/Tcl/8.6.4-foss-2016a/lib:/mnt/storage/easybuild/software/Java/1.8.0_72/lib:/mnt/storage/easybuild/software/libjpeg-turbo/1.4.2-foss-2016a/lib:/mnt/storage/easybuild/software/libpng/1.6.21-foss-2016a/lib:/mnt/storage/easybuild/software/libreadline/6.3-foss-2016a/lib:/mnt/storage/easybuild/software/ncurses/6.0-foss-2016a/lib:/mnt/storage/easybuild/software/bzip2/1.0.6-foss-2016a/lib:/mnt/storage/easybuild/software/GSL/2.3-foss-2017a/lib:/mnt/storage/easybuild/software/SQLite/3.13.0-GCC-5.4.0-2.26/lib:/mnt/storage/home/tk19812/software/lpsolve-5.5.0.10i/lib:/mnt/storage/home/tk19812/scratch/software/sparsehash/include:/mnt/storage/home/tk19812/scratch/software/bamtools/usr/local/lib64:/mnt/storage/home/tk19812/scratch/software/lzo-2.10/lib:/mnt/storage/home/tk19812/scratch/software/WiggleTools/lib:/mnt/storage/home/tk19812/scratch/software/cactus/lua-5.1.5/lib:/mnt/storage/home/tk19812/scratch/software/lzo-2.10/lib:/mnt/storage/home/tk19812/scratch/software/kyoto/lib:/mnt/storage/home/tk19812/scratch/software/swig-4.0.1/Lib:/mnt/storage/home/tk19812/scratch/software/openssl-1.1.1d/lib:/mnt/storage/home/tk19812/scratch/software/libBigWig/lib:/mnt/storage/home/tk19812/scratch/software/SuiteSparse/lib:/mnt/storage/home/tk19812/scratch/software/libuv-v1.37.0/.libs:/mnt/storage/home/tk19812/scratch/software/nghttp2-1.40.0/lib/.libs:/mnt/storage/home/tk19812/scratch/software/openldap/libraries/liblmdb:/mnt/storage/home/tk19812/scratch/CIRCOS/circos-0.69-9/libgd-2.3.0/lib:/mnt/storage/home/tk19812/scratch/software/jemalloc/lib:/mnt/storage/home/tk19812/.conda/envs/test3k/lib:/mnt/storage/home/tk19812/scratch/software/portcullis/lib/python3.7/site-packages:/mnt/storage/home/tk19812/scratch/software/portcullis/boost_1_67_0/stage/lib:/mnt/storage/home/tk19812/scratch/software/cactus/lib:no/lib -Wl,--as-needed -static -L../kyotocabinet -L/mnt/storage/home/tk19812/scratch/software/lzo-2.10/lib -L. -L/mnt/storage/home/tk19812/scratch/software/cactus/lib -L/usr/local/lib -L/mnt/storage/home/tk19812/scratch/software/cactus/lib -Lno/lib -Wl,-rpath-link,.:/usr/local/lib:.:/usr/local/lib:/mnt/storage/easybuild/software/HDF5/1.8.17-foss-2016b/lib:/mnt/storage/easybuild/software/Szip/2.1-foss-2016b/lib:/mnt/storage/easybuild/software/zlib/1.2.8-foss-2016b/lib:/mnt/storage/easybuild/software/ScaLAPACK/2.0.2-gompi-2016b-OpenBLAS-0.2.18-LAPACK-3.6.1/lib:/mnt/storage/easybuild/software/OpenBLAS/0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.1/lib:/mnt/storage/easybuild/software/FFTW/3.3.4-gompi-2016b/lib:/mnt/storage/easybuild/software/OpenMPI/1.10.3-GCC-5.4.0-2.26/lib:/mnt/storage/easybuild/software/hwloc/1.11.3-GCC-5.4.0-2.26/lib:/mnt/storage/easybuild/software/numactl/2.0.11-GCC-5.4.0-2.26/lib:/mnt/storage/easybuild/software/binutils/2.26-GCCcore-5.4.0/lib:/mnt/storage/easybuild/software/GCCcore/5.4.0/lib/gcc/x86_64-unknown-linux-gnu/5.4.0:/mnt/storage/easybuild/software/GCCcore/5.4.0/lib64:/mnt/storage/easybuild/software/GCCcore/5.4.0/lib:/mnt/storage/software/apps/ncbi-blast/gnu/2.7.1/lib:/mnt/storage/easybuild/software/R/3.2.3-foss-2016a/lib64/R/lib:/mnt/storage/easybuild/software/R/3.2.3-foss-2016a/lib64:/mnt/storage/easybuild/software/GMP/6.1.0-foss-2016a/lib:/mnt/storage/easybuild/software/PROJ/4.9.2-foss-2016a/lib:/mnt/storage/easybuild/software/GDAL/2.0.2-foss-2016a/lib:/mnt/storage/easybuild/software/expat/2.1.0-foss-2016a/lib:/mnt/storage/easybuild/software/netCDF/4.3.3.1-foss-2016a/lib64:/mnt/storage/easybuild/software/libxml2/2.9.3-foss-2016a/lib:/mnt/storage/easybuild/software/cURL/7.47.0-foss-2016a/lib:/mnt/storage/easybuild/software/Tk/8.6.4-foss-2016a-no-X11/lib:/mnt/storage/easybuild/software/Tcl/8.6.4-foss-2016a/lib:/mnt/storage/easybuild/software/Java/1.8.0_72/lib:/mnt/storage/easybuild/software/libjpeg-turbo/1.4.2-foss-2016a/lib:/mnt/storage/easybuild/software/libpng/1.6.21-foss-2016a/lib:/mnt/storage/easybuild/software/libreadline/6.3-foss-2016a/lib:/mnt/storage/easybuild/software/ncurses/6.0-foss-2016a/lib:/mnt/storage/easybuild/software/bzip2/1.0.6-foss-2016a/lib:/mnt/storage/easybuild/software/GSL/2.3-foss-2017a/lib:/mnt/storage/easybuild/software/SQLite/3.13.0-GCC-5.4.0-2.26/lib:/mnt/storage/home/tk19812/software/lpsolve-5.5.0.10i/lib:/mnt/storage/home/tk19812/scratch/software/sparsehash/include:/mnt/storage/home/tk19812/scratch/software/bamtools/usr/local/lib64:/mnt/storage/home/tk19812/scratch/software/lzo-2.10/lib:/mnt/storage/home/tk19812/scratch/software/WiggleTools/lib:/mnt/storage/home/tk19812/scratch/software/cactus/lua-5.1.5/lib:/mnt/storage/home/tk19812/scratch/software/lzo-2.10/lib:/mnt/storage/home/tk19812/scratch/software/kyoto/lib:/mnt/storage/home/tk19812/scratch/software/swig-4.0.1/Lib:/mnt/storage/home/tk19812/scratch/software/openssl-1.1.1d/lib:/mnt/storage/home/tk19812/scratch/software/libBigWig/lib:/mnt/storage/home/tk19812/scratch/software/SuiteSparse/lib:/mnt/storage/home/tk19812/scratch/software/libuv-v1.37.0/.libs:/mnt/storage/home/tk19812/scratch/software/nghttp2-1.40.0/lib/.libs:/mnt/storage/home/tk19812/scratch/software/openldap/libraries/liblmdb:/mnt/storage/home/tk19812/scratch/CIRCOS/circos-0.69-9/libgd-2.3.0/lib:/mnt/storage/home/tk19812/scratch/software/jemalloc/lib:/mnt/storage/home/tk19812/.conda/envs/test3k/lib:/mnt/storage/home/tk19812/scratch/software/portcullis/lib/python3.7/site-packages:/mnt/storage/home/tk19812/scratch/software/portcullis/boost_1_67_0/stage/lib:/mnt/storage/home/tk19812/scratch/software/cactus/lib:no/lib -Wl,--as-needed -lkyototycoon -lkyotocabinet -lkyotocabinet -llzma -llzo2 -lz -lstdc++ -lresolv -lnsl -ldl -lrt -lpthread -lm -lc  -lkyotocabinet -llzma -llzo2 -lz -lstdc++ -lresolv -lnsl -ldl -lrt -lpthread -lm -lc 
/mnt/storage/easybuild/software/binutils/2.26-GCCcore-5.4.0/bin/ld.gold: error: cannot find -llzma
/mnt/storage/easybuild/software/binutils/2.26-GCCcore-5.4.0/bin/ld.gold: error: cannot find -llzma
./libkyototycoon.a(ktsocket.o):ktsocket.cc:function kyototycoon::Socket::get_host_address(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&): warning: Using 'getaddrinfo' in statically linked applications requires at runtime the shared libraries from the glibc version used for linking
/lib/../lib64/libpthread.a(libpthread.o):function sem_open: warning: the use of `mktemp' is dangerous, better use `mkstemp'
collect2: error: ld returned 1 exit status
make[3]: *** [ktutiltest] Error 1
make[3]: *** Waiting for unfinished jobs....
/mnt/storage/easybuild/software/binutils/2.26-GCCcore-5.4.0/bin/ld.gold: error: cannot find -llzma
/mnt/storage/easybuild/software/binutils/2.26-GCCcore-5.4.0/bin/ld.gold: error: cannot find -llzma
/lib/../lib64/libpthread.a(libpthread.o):function sem_open: warning: the use of `mktemp' is dangerous, better use `mkstemp'
collect2: error: ld returned 1 exit status
make[3]: *** [kttimedtest] Error 1
/mnt/storage/easybuild/software/binutils/2.26-GCCcore-5.4.0/bin/ld.gold: error: cannot find -llzma
/mnt/storage/easybuild/software/binutils/2.26-GCCcore-5.4.0/bin/ld.gold: error: cannot find -llzma
./libkyototycoon.a(ktsocket.o):ktsocket.cc:function kyototycoon::Socket::get_host_address(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&): warning: Using 'getaddrinfo' in statically linked applications requires at runtime the shared libraries from the glibc version used for linking
/lib/../lib64/libpthread.a(libpthread.o):function sem_open: warning: the use of `mktemp' is dangerous, better use `mkstemp'
collect2: error: ld returned 1 exit status
make[3]: *** [ktutilmgr] Error 1
/mnt/storage/easybuild/software/binutils/2.26-GCCcore-5.4.0/bin/ld.gold: error: cannot find -llzma
/mnt/storage/easybuild/software/binutils/2.26-GCCcore-5.4.0/bin/ld.gold: error: cannot find -llzma
./libkyototycoon.a(ktsocket.o):ktsocket.cc:function kyototycoon::Socket::get_host_address(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&): warning: Using 'getaddrinfo' in statically linked applications requires at runtime the shared libraries from the glibc version used for linking
/lib/../lib64/libpthread.a(libpthread.o):function sem_open: warning: the use of `mktemp' is dangerous, better use `mkstemp'
collect2: error: ld returned 1 exit status
make[3]: *** [ktutilserv] Error 1
make[3]: Leaving directory `/mnt/storage/scratch/tk19812/software/cactus/submodules/kyoto/kyototycoon'
make[2]: *** [tycoon] Error 2
make[2]: Leaving directory `/mnt/storage/scratch/tk19812/software/cactus/submodules/kyoto'
make[1]: *** [suball.kyoto] Error 2
make[1]: Leaving directory `/mnt/storage/scratch/tk19812/software/cactus'
make: *** [all] Error 2

Any help? F

[diekhans]

These are all missing dependencies. Please use the precompiled distribution. A new release was just made.

Francesco Cicconardi notifications@github.com writes:

Hi Mark,

I'm trying to reinstall cactus, given you updates. But I'm having problems again:

#================================================================
# Ready to install.
#================================================================
make[3]: Leaving directory `/mnt/storage/scratch/tk19812/software/cactus/submodules/kyoto/kyotocabinet'
grep -q '^CPPFLAGS.*-D_KCDEBUG' kyotocabinet/Makefile || make -j4 -C kyotocabinet strip
make[3]: Entering directory `/mnt/storage/scratch/tk19812/software/cactus/submodules/kyoto/kyotocabinet'
make[3]: warning: -jN forced in submake: disabling jobserver mode.
strip kcutiltest kcutilmgr kcprototest kcstashtest kccachetest kcgrasstest kchashtest kchashmgr kctreetest kctreemgr kcdirtest kcdirmgr kcforesttest kcforestmgr kcpolytest kcpolymgr kclangctest
make[3]: Leaving directory `/mnt/storage/scratch/tk19812/software/cactus/submodules/kyoto/kyotocabinet'
make -j4 -C kyototycoon
make[3]: Entering directory `/mnt/storage/scratch/tk19812/software/cactus/submodules/kyoto/kyototycoon'
make[3]: warning: -jN forced in submake: disabling jobserver mode.
g++ -g -O2 -Wall -fPIC -fsigned-char -g0 -O2 -Wno-unused-but-set-variable -Wno-unused-but-set-parameter -o ktutiltest ktutiltest.o -L../kyotocabinet -L/mnt/storage/home/tk19812/scratch/software/lzo-2.10/lib -L. -L/mnt/storage/home/tk19812/scratch/software/cactus/lib -L/usr/local/lib -L/mnt/storage/home/tk19812/scratch/software/cactus/lib -Lno/lib -Wl,-rpath-link,.:/usr/local/lib:.:/usr/local/lib:/mnt/storage/easybuild/software/HDF5/1.8.17-foss-2016b/lib:/mnt/storage/easybuild/software/Szip/2.1-foss-2016b/lib:/mnt/storage/easybuild/software/zlib/1.2.8-foss-2016b/lib:/mnt/storage/easybuild/software/ScaLAPACK/2.0.2-gompi-2016b-OpenBLAS-0.2.18-LAPACK-3.6.1/lib:/mnt/storage/easybuild/software/OpenBLAS/0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.1/lib:/mnt/storage/easybuild/software/FFTW/3.3.4-gompi-2016b/lib:/mnt/storage/easybuild/software/OpenMPI/1.10.3-GCC-5.4.0-2.26/lib:/mnt/storage/easybuild/software/hwloc/1.11.3-GCC-5.4.0-2.26/lib:/mnt/storage/easybuild/software/numactl/2.0.11-GCC-5.4.0-2.26/lib:/mnt/storage/easybuild/software/binutils/2.26-GCCcore-5.4.0/lib:/mnt/storage/easybuild/software/GCCcore/5.4.0/lib/gcc/x86_64-unknown-linux-gnu/5.4.0:/mnt/storage/easybuild/software/GCCcore/5.4.0/lib64:/mnt/storage/easybuild/software/GCCcore/5.4.0/lib:/mnt/storage/software/apps/ncbi-blast/gnu/2.7.1/lib:/mnt/storage/easybuild/software/R/3.2.3-foss-2016a/lib64/R/lib:/mnt/storage/easybuild/software/R/3.2.3-foss-2016a/lib64:/mnt/storage/easybuild/software/GMP/6.1.0-foss-2016a/lib:/mnt/storage/easybuild/software/PROJ/4.9.2-foss-2016a/lib:/mnt/storage/easybuild/software/GDAL/2.0.2-foss-2016a/lib:/mnt/storage/easybuild/software/expat/2.1.0-foss-2016a/lib:/mnt/storage/easybuild/software/netCDF/4.3.3.1-foss-2016a/lib64:/mnt/storage/easybuild/software/libxml2/2.9.3-foss-2016a/lib:/mnt/storage/easybuild/software/cURL/7.47.0-foss-2016a/lib:/mnt/storage/easybuild/software/Tk/8.6.4-foss-2016a-no-X11/lib:/mnt/storage/easybuild/software/Tcl/8.6.4-foss-2016a/lib:/mnt/storage/easybuild/software/Java/1.8.0_72/lib:/mnt/storage/easybuild/software/libjpeg-turbo/1.4.2-foss-2016a/lib:/mnt/storage/easybuild/software/libpng/1.6.21-foss-2016a/lib:/mnt/storage/easybuild/software/libreadline/6.3-foss-2016a/lib:/mnt/storage/easybuild/software/ncurses/6.0-foss-2016a/lib:/mnt/storage/easybuild/software/bzip2/1.0.6-foss-2016a/lib:/mnt/storage/easybuild/software/GSL/2.3-foss-2017a/lib:/mnt/storage/easybuild/software/SQLite/3.13.0-GCC-5.4.0-2.26/lib:/mnt/storage/home/tk19812/software/lpsolve-5.5.0.10i/lib:/mnt/storage/home/tk19812/scratch/software/sparsehash/include:/mnt/storage/home/tk19812/scratch/software/bamtools/usr/local/lib64:/mnt/storage/home/tk19812/scratch/software/lzo-2.10/lib:/mnt/storage/home/tk19812/scratch/software/WiggleTools/lib:/mnt/storage/home/tk19812/scratch/software/cactus/lua-5.1.5/lib:/mnt/storage/home/tk19812/scratch/software/lzo-2.10/lib:/mnt/storage/home/tk19812/scratch/software/kyoto/lib:/mnt/storage/home/tk19812/scratch/software/swig-4.0.1/Lib:/mnt/storage/home/tk19812/scratch/software/openssl-1.1.1d/lib:/mnt/storage/home/tk19812/scratch/software/libBigWig/lib:/mnt/storage/home/tk19812/scratch/software/SuiteSparse/lib:/mnt/storage/home/tk19812/scratch/software/libuv-v1.37.0/.libs:/mnt/storage/home/tk19812/scratch/software/nghttp2-1.40.0/lib/.libs:/mnt/storage/home/tk19812/scratch/software/openldap/libraries/liblmdb:/mnt/storage/home/tk19812/scratch/CIRCOS/circos-0.69-9/libgd-2.3.0/lib:/mnt/storage/home/tk19812/scratch/software/jemalloc/lib:/mnt/storage/home/tk19812/.conda/envs/test3k/lib:/mnt/storage/home/tk19812/scratch/software/portcullis/lib/python3.7/site-packages:/mnt/storage/home/tk19812/scratch/software/portcullis/boost_1_67_0/stage/lib:/mnt/storage/home/tk19812/scratch/software/cactus/lib:no/lib -Wl,--as-needed -static -L../kyotocabinet -L/mnt/storage/home/tk19812/scratch/software/lzo-2.10/lib -L. -L/mnt/storage/home/tk19812/scratch/software/cactus/lib -L/usr/local/lib -L/mnt/storage/home/tk19812/scratch/software/cactus/lib -Lno/lib -Wl,-rpath-link,.:/usr/local/lib:.:/usr/local/lib:/mnt/storage/easybuild/software/HDF5/1.8.17-foss-2016b/lib:/mnt/storage/easybuild/software/Szip/2.1-foss-2016b/lib:/mnt/storage/easybuild/software/zlib/1.2.8-foss-2016b/lib:/mnt/storage/easybuild/software/ScaLAPACK/2.0.2-gompi-2016b-OpenBLAS-0.2.18-LAPACK-3.6.1/lib:/mnt/storage/easybuild/software/OpenBLAS/0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.1/lib:/mnt/storage/easybuild/software/FFTW/3.3.4-gompi-2016b/lib:/mnt/storage/easybuild/software/OpenMPI/1.10.3-GCC-5.4.0-2.26/lib:/mnt/storage/easybuild/software/hwloc/1.11.3-GCC-5.4.0-2.26/lib:/mnt/storage/easybuild/software/numactl/2.0.11-GCC-5.4.0-2.26/lib:/mnt/storage/easybuild/software/binutils/2.26-GCCcore-5.4.0/lib:/mnt/storage/easybuild/software/GCCcore/5.4.0/lib/gcc/x86_64-unknown-linux-gnu/5.4.0:/mnt/storage/easybuild/software/GCCcore/5.4.0/lib64:/mnt/storage/easybuild/software/GCCcore/5.4.0/lib:/mnt/storage/software/apps/ncbi-blast/gnu/2.7.1/lib:/mnt/storage/easybuild/software/R/3.2.3-foss-2016a/lib64/R/lib:/mnt/storage/easybuild/software/R/3.2.3-foss-2016a/lib64:/mnt/storage/easybuild/software/GMP/6.1.0-foss-2016a/lib:/mnt/storage/easybuild/software/PROJ/4.9.2-foss-2016a/lib:/mnt/storage/easybuild/software/GDAL/2.0.2-foss-2016a/lib:/mnt/storage/easybuild/software/expat/2.1.0-foss-2016a/lib:/mnt/storage/easybuild/software/netCDF/4.3.3.1-foss-2016a/lib64:/mnt/storage/easybuild/software/libxml2/2.9.3-foss-2016a/lib:/mnt/storage/easybuild/software/cURL/7.47.0-foss-2016a/lib:/mnt/storage/easybuild/software/Tk/8.6.4-foss-2016a-no-X11/lib:/mnt/storage/easybuild/software/Tcl/8.6.4-foss-2016a/lib:/mnt/storage/easybuild/software/Java/1.8.0_72/lib:/mnt/storage/easybuild/software/libjpeg-turbo/1.4.2-foss-2016a/lib:/mnt/storage/easybuild/software/libpng/1.6.21-foss-2016a/lib:/mnt/storage/easybuild/software/libreadline/6.3-foss-2016a/lib:/mnt/storage/easybuild/software/ncurses/6.0-foss-2016a/lib:/mnt/storage/easybuild/software/bzip2/1.0.6-foss-2016a/lib:/mnt/storage/easybuild/software/GSL/2.3-foss-2017a/lib:/mnt/storage/easybuild/software/SQLite/3.13.0-GCC-5.4.0-2.26/lib:/mnt/storage/home/tk19812/software/lpsolve-5.5.0.10i/lib:/mnt/storage/home/tk19812/scratch/software/sparsehash/include:/mnt/storage/home/tk19812/scratch/software/bamtools/usr/local/lib64:/mnt/storage/home/tk19812/scratch/software/lzo-2.10/lib:/mnt/storage/home/tk19812/scratch/software/WiggleTools/lib:/mnt/storage/home/tk19812/scratch/software/cactus/lua-5.1.5/lib:/mnt/storage/home/tk19812/scratch/software/lzo-2.10/lib:/mnt/storage/home/tk19812/scratch/software/kyoto/lib:/mnt/storage/home/tk19812/scratch/software/swig-4.0.1/Lib:/mnt/storage/home/tk19812/scratch/software/openssl-1.1.1d/lib:/mnt/storage/home/tk19812/scratch/software/libBigWig/lib:/mnt/storage/home/tk19812/scratch/software/SuiteSparse/lib:/mnt/storage/home/tk19812/scratch/software/libuv-v1.37.0/.libs:/mnt/storage/home/tk19812/scratch/software/nghttp2-1.40.0/lib/.libs:/mnt/storage/home/tk19812/scratch/software/openldap/libraries/liblmdb:/mnt/storage/home/tk19812/scratch/CIRCOS/circos-0.69-9/libgd-2.3.0/lib:/mnt/storage/home/tk19812/scratch/software/jemalloc/lib:/mnt/storage/home/tk19812/.conda/envs/test3k/lib:/mnt/storage/home/tk19812/scratch/software/portcullis/lib/python3.7/site-packages:/mnt/storage/home/tk19812/scratch/software/portcullis/boost_1_67_0/stage/lib:/mnt/storage/home/tk19812/scratch/software/cactus/lib:no/lib -Wl,--as-needed -lkyototycoon -lkyotocabinet -lkyotocabinet -llzma -llzo2 -lz -lstdc++ -lresolv -lnsl -ldl -lrt -lpthread -lm -lc  -lkyotocabinet -llzma -llzo2 -lz -lstdc++ -lresolv -lnsl -ldl -lrt -lpthread -lm -lc 
g++ -g -O2 -Wall -fPIC -fsigned-char -g0 -O2 -Wno-unused-but-set-variable -Wno-unused-but-set-parameter -o ktutilmgr ktutilmgr.o -L../kyotocabinet -L/mnt/storage/home/tk19812/scratch/software/lzo-2.10/lib -L. -L/mnt/storage/home/tk19812/scratch/software/cactus/lib -L/usr/local/lib -L/mnt/storage/home/tk19812/scratch/software/cactus/lib -Lno/lib -Wl,-rpath-link,.:/usr/local/lib:.:/usr/local/lib:/mnt/storage/easybuild/software/HDF5/1.8.17-foss-2016b/lib:/mnt/storage/easybuild/software/Szip/2.1-foss-2016b/lib:/mnt/storage/easybuild/software/zlib/1.2.8-foss-2016b/lib:/mnt/storage/easybuild/software/ScaLAPACK/2.0.2-gompi-2016b-OpenBLAS-0.2.18-LAPACK-3.6.1/lib:/mnt/storage/easybuild/software/OpenBLAS/0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.1/lib:/mnt/storage/easybuild/software/FFTW/3.3.4-gompi-2016b/lib:/mnt/storage/easybuild/software/OpenMPI/1.10.3-GCC-5.4.0-2.26/lib:/mnt/storage/easybuild/software/hwloc/1.11.3-GCC-5.4.0-2.26/lib:/mnt/storage/easybuild/software/numactl/2.0.11-GCC-5.4.0-2.26/lib:/mnt/storage/easybuild/software/binutils/2.26-GCCcore-5.4.0/lib:/mnt/storage/easybuild/software/GCCcore/5.4.0/lib/gcc/x86_64-unknown-linux-gnu/5.4.0:/mnt/storage/easybuild/software/GCCcore/5.4.0/lib64:/mnt/storage/easybuild/software/GCCcore/5.4.0/lib:/mnt/storage/software/apps/ncbi-blast/gnu/2.7.1/lib:/mnt/storage/easybuild/software/R/3.2.3-foss-2016a/lib64/R/lib:/mnt/storage/easybuild/software/R/3.2.3-foss-2016a/lib64:/mnt/storage/easybuild/software/GMP/6.1.0-foss-2016a/lib:/mnt/storage/easybuild/software/PROJ/4.9.2-foss-2016a/lib:/mnt/storage/easybuild/software/GDAL/2.0.2-foss-2016a/lib:/mnt/storage/easybuild/software/expat/2.1.0-foss-2016a/lib:/mnt/storage/easybuild/software/netCDF/4.3.3.1-foss-2016a/lib64:/mnt/storage/easybuild/software/libxml2/2.9.3-foss-2016a/lib:/mnt/storage/easybuild/software/cURL/7.47.0-foss-2016a/lib:/mnt/storage/easybuild/software/Tk/8.6.4-foss-2016a-no-X11/lib:/mnt/storage/easybuild/software/Tcl/8.6.4-foss-2016a/lib:/mnt/storage/easybuild/software/Java/1.8.0_72/lib:/mnt/storage/easybuild/software/libjpeg-turbo/1.4.2-foss-2016a/lib:/mnt/storage/easybuild/software/libpng/1.6.21-foss-2016a/lib:/mnt/storage/easybuild/software/libreadline/6.3-foss-2016a/lib:/mnt/storage/easybuild/software/ncurses/6.0-foss-2016a/lib:/mnt/storage/easybuild/software/bzip2/1.0.6-foss-2016a/lib:/mnt/storage/easybuild/software/GSL/2.3-foss-2017a/lib:/mnt/storage/easybuild/software/SQLite/3.13.0-GCC-5.4.0-2.26/lib:/mnt/storage/home/tk19812/software/lpsolve-5.5.0.10i/lib:/mnt/storage/home/tk19812/scratch/software/sparsehash/include:/mnt/storage/home/tk19812/scratch/software/bamtools/usr/local/lib64:/mnt/storage/home/tk19812/scratch/software/lzo-2.10/lib:/mnt/storage/home/tk19812/scratch/software/WiggleTools/lib:/mnt/storage/home/tk19812/scratch/software/cactus/lua-5.1.5/lib:/mnt/storage/home/tk19812/scratch/software/lzo-2.10/lib:/mnt/storage/home/tk19812/scratch/software/kyoto/lib:/mnt/storage/home/tk19812/scratch/software/swig-4.0.1/Lib:/mnt/storage/home/tk19812/scratch/software/openssl-1.1.1d/lib:/mnt/storage/home/tk19812/scratch/software/libBigWig/lib:/mnt/storage/home/tk19812/scratch/software/SuiteSparse/lib:/mnt/storage/home/tk19812/scratch/software/libuv-v1.37.0/.libs:/mnt/storage/home/tk19812/scratch/software/nghttp2-1.40.0/lib/.libs:/mnt/storage/home/tk19812/scratch/software/openldap/libraries/liblmdb:/mnt/storage/home/tk19812/scratch/CIRCOS/circos-0.69-9/libgd-2.3.0/lib:/mnt/storage/home/tk19812/scratch/software/jemalloc/lib:/mnt/storage/home/tk19812/.conda/envs/test3k/lib:/mnt/storage/home/tk19812/scratch/software/portcullis/lib/python3.7/site-packages:/mnt/storage/home/tk19812/scratch/software/portcullis/boost_1_67_0/stage/lib:/mnt/storage/home/tk19812/scratch/software/cactus/lib:no/lib -Wl,--as-needed -static -L../kyotocabinet -L/mnt/storage/home/tk19812/scratch/software/lzo-2.10/lib -L. -L/mnt/storage/home/tk19812/scratch/software/cactus/lib -L/usr/local/lib -L/mnt/storage/home/tk19812/scratch/software/cactus/lib -Lno/lib -Wl,-rpath-link,.:/usr/local/lib:.:/usr/local/lib:/mnt/storage/easybuild/software/HDF5/1.8.17-foss-2016b/lib:/mnt/storage/easybuild/software/Szip/2.1-foss-2016b/lib:/mnt/storage/easybuild/software/zlib/1.2.8-foss-2016b/lib:/mnt/storage/easybuild/software/ScaLAPACK/2.0.2-gompi-2016b-OpenBLAS-0.2.18-LAPACK-3.6.1/lib:/mnt/storage/easybuild/software/OpenBLAS/0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.1/lib:/mnt/storage/easybuild/software/FFTW/3.3.4-gompi-2016b/lib:/mnt/storage/easybuild/software/OpenMPI/1.10.3-GCC-5.4.0-2.26/lib:/mnt/storage/easybuild/software/hwloc/1.11.3-GCC-5.4.0-2.26/lib:/mnt/storage/easybuild/software/numactl/2.0.11-GCC-5.4.0-2.26/lib:/mnt/storage/easybuild/software/binutils/2.26-GCCcore-5.4.0/lib:/mnt/storage/easybuild/software/GCCcore/5.4.0/lib/gcc/x86_64-unknown-linux-gnu/5.4.0:/mnt/storage/easybuild/software/GCCcore/5.4.0/lib64:/mnt/storage/easybuild/software/GCCcore/5.4.0/lib:/mnt/storage/software/apps/ncbi-blast/gnu/2.7.1/lib:/mnt/storage/easybuild/software/R/3.2.3-foss-2016a/lib64/R/lib:/mnt/storage/easybuild/software/R/3.2.3-foss-2016a/lib64:/mnt/storage/easybuild/software/GMP/6.1.0-foss-2016a/lib:/mnt/storage/easybuild/software/PROJ/4.9.2-foss-2016a/lib:/mnt/storage/easybuild/software/GDAL/2.0.2-foss-2016a/lib:/mnt/storage/easybuild/software/expat/2.1.0-foss-2016a/lib:/mnt/storage/easybuild/software/netCDF/4.3.3.1-foss-2016a/lib64:/mnt/storage/easybuild/software/libxml2/2.9.3-foss-2016a/lib:/mnt/storage/easybuild/software/cURL/7.47.0-foss-2016a/lib:/mnt/storage/easybuild/software/Tk/8.6.4-foss-2016a-no-X11/lib:/mnt/storage/easybuild/software/Tcl/8.6.4-foss-2016a/lib:/mnt/storage/easybuild/software/Java/1.8.0_72/lib:/mnt/storage/easybuild/software/libjpeg-turbo/1.4.2-foss-2016a/lib:/mnt/storage/easybuild/software/libpng/1.6.21-foss-2016a/lib:/mnt/storage/easybuild/software/libreadline/6.3-foss-2016a/lib:/mnt/storage/easybuild/software/ncurses/6.0-foss-2016a/lib:/mnt/storage/easybuild/software/bzip2/1.0.6-foss-2016a/lib:/mnt/storage/easybuild/software/GSL/2.3-foss-2017a/lib:/mnt/storage/easybuild/software/SQLite/3.13.0-GCC-5.4.0-2.26/lib:/mnt/storage/home/tk19812/software/lpsolve-5.5.0.10i/lib:/mnt/storage/home/tk19812/scratch/software/sparsehash/include:/mnt/storage/home/tk19812/scratch/software/bamtools/usr/local/lib64:/mnt/storage/home/tk19812/scratch/software/lzo-2.10/lib:/mnt/storage/home/tk19812/scratch/software/WiggleTools/lib:/mnt/storage/home/tk19812/scratch/software/cactus/lua-5.1.5/lib:/mnt/storage/home/tk19812/scratch/software/lzo-2.10/lib:/mnt/storage/home/tk19812/scratch/software/kyoto/lib:/mnt/storage/home/tk19812/scratch/software/swig-4.0.1/Lib:/mnt/storage/home/tk19812/scratch/software/openssl-1.1.1d/lib:/mnt/storage/home/tk19812/scratch/software/libBigWig/lib:/mnt/storage/home/tk19812/scratch/software/SuiteSparse/lib:/mnt/storage/home/tk19812/scratch/software/libuv-v1.37.0/.libs:/mnt/storage/home/tk19812/scratch/software/nghttp2-1.40.0/lib/.libs:/mnt/storage/home/tk19812/scratch/software/openldap/libraries/liblmdb:/mnt/storage/home/tk19812/scratch/CIRCOS/circos-0.69-9/libgd-2.3.0/lib:/mnt/storage/home/tk19812/scratch/software/jemalloc/lib:/mnt/storage/home/tk19812/.conda/envs/test3k/lib:/mnt/storage/home/tk19812/scratch/software/portcullis/lib/python3.7/site-packages:/mnt/storage/home/tk19812/scratch/software/portcullis/boost_1_67_0/stage/lib:/mnt/storage/home/tk19812/scratch/software/cactus/lib:no/lib -Wl,--as-needed -lkyototycoon -lkyotocabinet -lkyotocabinet -llzma -llzo2 -lz -lstdc++ -lresolv -lnsl -ldl -lrt -lpthread -lm -lc  -lkyotocabinet -llzma -llzo2 -lz -lstdc++ -lresolv -lnsl -ldl -lrt -lpthread -lm -lc 
g++ -g -O2 -Wall -fPIC -fsigned-char -g0 -O2 -Wno-unused-but-set-variable -Wno-unused-but-set-parameter -o ktutilserv ktutilserv.o -L../kyotocabinet -L/mnt/storage/home/tk19812/scratch/software/lzo-2.10/lib -L. -L/mnt/storage/home/tk19812/scratch/software/cactus/lib -L/usr/local/lib -L/mnt/storage/home/tk19812/scratch/software/cactus/lib -Lno/lib -Wl,-rpath-link,.:/usr/local/lib:.:/usr/local/lib:/mnt/storage/easybuild/software/HDF5/1.8.17-foss-2016b/lib:/mnt/storage/easybuild/software/Szip/2.1-foss-2016b/lib:/mnt/storage/easybuild/software/zlib/1.2.8-foss-2016b/lib:/mnt/storage/easybuild/software/ScaLAPACK/2.0.2-gompi-2016b-OpenBLAS-0.2.18-LAPACK-3.6.1/lib:/mnt/storage/easybuild/software/OpenBLAS/0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.1/lib:/mnt/storage/easybuild/software/FFTW/3.3.4-gompi-2016b/lib:/mnt/storage/easybuild/software/OpenMPI/1.10.3-GCC-5.4.0-2.26/lib:/mnt/storage/easybuild/software/hwloc/1.11.3-GCC-5.4.0-2.26/lib:/mnt/storage/easybuild/software/numactl/2.0.11-GCC-5.4.0-2.26/lib:/mnt/storage/easybuild/software/binutils/2.26-GCCcore-5.4.0/lib:/mnt/storage/easybuild/software/GCCcore/5.4.0/lib/gcc/x86_64-unknown-linux-gnu/5.4.0:/mnt/storage/easybuild/software/GCCcore/5.4.0/lib64:/mnt/storage/easybuild/software/GCCcore/5.4.0/lib:/mnt/storage/software/apps/ncbi-blast/gnu/2.7.1/lib:/mnt/storage/easybuild/software/R/3.2.3-foss-2016a/lib64/R/lib:/mnt/storage/easybuild/software/R/3.2.3-foss-2016a/lib64:/mnt/storage/easybuild/software/GMP/6.1.0-foss-2016a/lib:/mnt/storage/easybuild/software/PROJ/4.9.2-foss-2016a/lib:/mnt/storage/easybuild/software/GDAL/2.0.2-foss-2016a/lib:/mnt/storage/easybuild/software/expat/2.1.0-foss-2016a/lib:/mnt/storage/easybuild/software/netCDF/4.3.3.1-foss-2016a/lib64:/mnt/storage/easybuild/software/libxml2/2.9.3-foss-2016a/lib:/mnt/storage/easybuild/software/cURL/7.47.0-foss-2016a/lib:/mnt/storage/easybuild/software/Tk/8.6.4-foss-2016a-no-X11/lib:/mnt/storage/easybuild/software/Tcl/8.6.4-foss-2016a/lib:/mnt/storage/easybuild/software/Java/1.8.0_72/lib:/mnt/storage/easybuild/software/libjpeg-turbo/1.4.2-foss-2016a/lib:/mnt/storage/easybuild/software/libpng/1.6.21-foss-2016a/lib:/mnt/storage/easybuild/software/libreadline/6.3-foss-2016a/lib:/mnt/storage/easybuild/software/ncurses/6.0-foss-2016a/lib:/mnt/storage/easybuild/software/bzip2/1.0.6-foss-2016a/lib:/mnt/storage/easybuild/software/GSL/2.3-foss-2017a/lib:/mnt/storage/easybuild/software/SQLite/3.13.0-GCC-5.4.0-2.26/lib:/mnt/storage/home/tk19812/software/lpsolve-5.5.0.10i/lib:/mnt/storage/home/tk19812/scratch/software/sparsehash/include:/mnt/storage/home/tk19812/scratch/software/bamtools/usr/local/lib64:/mnt/storage/home/tk19812/scratch/software/lzo-2.10/lib:/mnt/storage/home/tk19812/scratch/software/WiggleTools/lib:/mnt/storage/home/tk19812/scratch/software/cactus/lua-5.1.5/lib:/mnt/storage/home/tk19812/scratch/software/lzo-2.10/lib:/mnt/storage/home/tk19812/scratch/software/kyoto/lib:/mnt/storage/home/tk19812/scratch/software/swig-4.0.1/Lib:/mnt/storage/home/tk19812/scratch/software/openssl-1.1.1d/lib:/mnt/storage/home/tk19812/scratch/software/libBigWig/lib:/mnt/storage/home/tk19812/scratch/software/SuiteSparse/lib:/mnt/storage/home/tk19812/scratch/software/libuv-v1.37.0/.libs:/mnt/storage/home/tk19812/scratch/software/nghttp2-1.40.0/lib/.libs:/mnt/storage/home/tk19812/scratch/software/openldap/libraries/liblmdb:/mnt/storage/home/tk19812/scratch/CIRCOS/circos-0.69-9/libgd-2.3.0/lib:/mnt/storage/home/tk19812/scratch/software/jemalloc/lib:/mnt/storage/home/tk19812/.conda/envs/test3k/lib:/mnt/storage/home/tk19812/scratch/software/portcullis/lib/python3.7/site-packages:/mnt/storage/home/tk19812/scratch/software/portcullis/boost_1_67_0/stage/lib:/mnt/storage/home/tk19812/scratch/software/cactus/lib:no/lib -Wl,--as-needed -static -L../kyotocabinet -L/mnt/storage/home/tk19812/scratch/software/lzo-2.10/lib -L. -L/mnt/storage/home/tk19812/scratch/software/cactus/lib -L/usr/local/lib -L/mnt/storage/home/tk19812/scratch/software/cactus/lib -Lno/lib -Wl,-rpath-link,.:/usr/local/lib:.:/usr/local/lib:/mnt/storage/easybuild/software/HDF5/1.8.17-foss-2016b/lib:/mnt/storage/easybuild/software/Szip/2.1-foss-2016b/lib:/mnt/storage/easybuild/software/zlib/1.2.8-foss-2016b/lib:/mnt/storage/easybuild/software/ScaLAPACK/2.0.2-gompi-2016b-OpenBLAS-0.2.18-LAPACK-3.6.1/lib:/mnt/storage/easybuild/software/OpenBLAS/0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.1/lib:/mnt/storage/easybuild/software/FFTW/3.3.4-gompi-2016b/lib:/mnt/storage/easybuild/software/OpenMPI/1.10.3-GCC-5.4.0-2.26/lib:/mnt/storage/easybuild/software/hwloc/1.11.3-GCC-5.4.0-2.26/lib:/mnt/storage/easybuild/software/numactl/2.0.11-GCC-5.4.0-2.26/lib:/mnt/storage/easybuild/software/binutils/2.26-GCCcore-5.4.0/lib:/mnt/storage/easybuild/software/GCCcore/5.4.0/lib/gcc/x86_64-unknown-linux-gnu/5.4.0:/mnt/storage/easybuild/software/GCCcore/5.4.0/lib64:/mnt/storage/easybuild/software/GCCcore/5.4.0/lib:/mnt/storage/software/apps/ncbi-blast/gnu/2.7.1/lib:/mnt/storage/easybuild/software/R/3.2.3-foss-2016a/lib64/R/lib:/mnt/storage/easybuild/software/R/3.2.3-foss-2016a/lib64:/mnt/storage/easybuild/software/GMP/6.1.0-foss-2016a/lib:/mnt/storage/easybuild/software/PROJ/4.9.2-foss-2016a/lib:/mnt/storage/easybuild/software/GDAL/2.0.2-foss-2016a/lib:/mnt/storage/easybuild/software/expat/2.1.0-foss-2016a/lib:/mnt/storage/easybuild/software/netCDF/4.3.3.1-foss-2016a/lib64:/mnt/storage/easybuild/software/libxml2/2.9.3-foss-2016a/lib:/mnt/storage/easybuild/software/cURL/7.47.0-foss-2016a/lib:/mnt/storage/easybuild/software/Tk/8.6.4-foss-2016a-no-X11/lib:/mnt/storage/easybuild/software/Tcl/8.6.4-foss-2016a/lib:/mnt/storage/easybuild/software/Java/1.8.0_72/lib:/mnt/storage/easybuild/software/libjpeg-turbo/1.4.2-foss-2016a/lib:/mnt/storage/easybuild/software/libpng/1.6.21-foss-2016a/lib:/mnt/storage/easybuild/software/libreadline/6.3-foss-2016a/lib:/mnt/storage/easybuild/software/ncurses/6.0-foss-2016a/lib:/mnt/storage/easybuild/software/bzip2/1.0.6-foss-2016a/lib:/mnt/storage/easybuild/software/GSL/2.3-foss-2017a/lib:/mnt/storage/easybuild/software/SQLite/3.13.0-GCC-5.4.0-2.26/lib:/mnt/storage/home/tk19812/software/lpsolve-5.5.0.10i/lib:/mnt/storage/home/tk19812/scratch/software/sparsehash/include:/mnt/storage/home/tk19812/scratch/software/bamtools/usr/local/lib64:/mnt/storage/home/tk19812/scratch/software/lzo-2.10/lib:/mnt/storage/home/tk19812/scratch/software/WiggleTools/lib:/mnt/storage/home/tk19812/scratch/software/cactus/lua-5.1.5/lib:/mnt/storage/home/tk19812/scratch/software/lzo-2.10/lib:/mnt/storage/home/tk19812/scratch/software/kyoto/lib:/mnt/storage/home/tk19812/scratch/software/swig-4.0.1/Lib:/mnt/storage/home/tk19812/scratch/software/openssl-1.1.1d/lib:/mnt/storage/home/tk19812/scratch/software/libBigWig/lib:/mnt/storage/home/tk19812/scratch/software/SuiteSparse/lib:/mnt/storage/home/tk19812/scratch/software/libuv-v1.37.0/.libs:/mnt/storage/home/tk19812/scratch/software/nghttp2-1.40.0/lib/.libs:/mnt/storage/home/tk19812/scratch/software/openldap/libraries/liblmdb:/mnt/storage/home/tk19812/scratch/CIRCOS/circos-0.69-9/libgd-2.3.0/lib:/mnt/storage/home/tk19812/scratch/software/jemalloc/lib:/mnt/storage/home/tk19812/.conda/envs/test3k/lib:/mnt/storage/home/tk19812/scratch/software/portcullis/lib/python3.7/site-packages:/mnt/storage/home/tk19812/scratch/software/portcullis/boost_1_67_0/stage/lib:/mnt/storage/home/tk19812/scratch/software/cactus/lib:no/lib -Wl,--as-needed -lkyototycoon -lkyotocabinet -lkyotocabinet -llzma -llzo2 -lz -lstdc++ -lresolv -lnsl -ldl -lrt -lpthread -lm -lc  -lkyotocabinet -llzma -llzo2 -lz -lstdc++ -lresolv -lnsl -ldl -lrt -lpthread -lm -lc 
g++ -g -O2 -Wall -fPIC -fsigned-char -g0 -O2 -Wno-unused-but-set-variable -Wno-unused-but-set-parameter -o kttimedtest kttimedtest.o -L../kyotocabinet -L/mnt/storage/home/tk19812/scratch/software/lzo-2.10/lib -L. -L/mnt/storage/home/tk19812/scratch/software/cactus/lib -L/usr/local/lib -L/mnt/storage/home/tk19812/scratch/software/cactus/lib -Lno/lib -Wl,-rpath-link,.:/usr/local/lib:.:/usr/local/lib:/mnt/storage/easybuild/software/HDF5/1.8.17-foss-2016b/lib:/mnt/storage/easybuild/software/Szip/2.1-foss-2016b/lib:/mnt/storage/easybuild/software/zlib/1.2.8-foss-2016b/lib:/mnt/storage/easybuild/software/ScaLAPACK/2.0.2-gompi-2016b-OpenBLAS-0.2.18-LAPACK-3.6.1/lib:/mnt/storage/easybuild/software/OpenBLAS/0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.1/lib:/mnt/storage/easybuild/software/FFTW/3.3.4-gompi-2016b/lib:/mnt/storage/easybuild/software/OpenMPI/1.10.3-GCC-5.4.0-2.26/lib:/mnt/storage/easybuild/software/hwloc/1.11.3-GCC-5.4.0-2.26/lib:/mnt/storage/easybuild/software/numactl/2.0.11-GCC-5.4.0-2.26/lib:/mnt/storage/easybuild/software/binutils/2.26-GCCcore-5.4.0/lib:/mnt/storage/easybuild/software/GCCcore/5.4.0/lib/gcc/x86_64-unknown-linux-gnu/5.4.0:/mnt/storage/easybuild/software/GCCcore/5.4.0/lib64:/mnt/storage/easybuild/software/GCCcore/5.4.0/lib:/mnt/storage/software/apps/ncbi-blast/gnu/2.7.1/lib:/mnt/storage/easybuild/software/R/3.2.3-foss-2016a/lib64/R/lib:/mnt/storage/easybuild/software/R/3.2.3-foss-2016a/lib64:/mnt/storage/easybuild/software/GMP/6.1.0-foss-2016a/lib:/mnt/storage/easybuild/software/PROJ/4.9.2-foss-2016a/lib:/mnt/storage/easybuild/software/GDAL/2.0.2-foss-2016a/lib:/mnt/storage/easybuild/software/expat/2.1.0-foss-2016a/lib:/mnt/storage/easybuild/software/netCDF/4.3.3.1-foss-2016a/lib64:/mnt/storage/easybuild/software/libxml2/2.9.3-foss-2016a/lib:/mnt/storage/easybuild/software/cURL/7.47.0-foss-2016a/lib:/mnt/storage/easybuild/software/Tk/8.6.4-foss-2016a-no-X11/lib:/mnt/storage/easybuild/software/Tcl/8.6.4-foss-2016a/lib:/mnt/storage/easybuild/software/Java/1.8.0_72/lib:/mnt/storage/easybuild/software/libjpeg-turbo/1.4.2-foss-2016a/lib:/mnt/storage/easybuild/software/libpng/1.6.21-foss-2016a/lib:/mnt/storage/easybuild/software/libreadline/6.3-foss-2016a/lib:/mnt/storage/easybuild/software/ncurses/6.0-foss-2016a/lib:/mnt/storage/easybuild/software/bzip2/1.0.6-foss-2016a/lib:/mnt/storage/easybuild/software/GSL/2.3-foss-2017a/lib:/mnt/storage/easybuild/software/SQLite/3.13.0-GCC-5.4.0-2.26/lib:/mnt/storage/home/tk19812/software/lpsolve-5.5.0.10i/lib:/mnt/storage/home/tk19812/scratch/software/sparsehash/include:/mnt/storage/home/tk19812/scratch/software/bamtools/usr/local/lib64:/mnt/storage/home/tk19812/scratch/software/lzo-2.10/lib:/mnt/storage/home/tk19812/scratch/software/WiggleTools/lib:/mnt/storage/home/tk19812/scratch/software/cactus/lua-5.1.5/lib:/mnt/storage/home/tk19812/scratch/software/lzo-2.10/lib:/mnt/storage/home/tk19812/scratch/software/kyoto/lib:/mnt/storage/home/tk19812/scratch/software/swig-4.0.1/Lib:/mnt/storage/home/tk19812/scratch/software/openssl-1.1.1d/lib:/mnt/storage/home/tk19812/scratch/software/libBigWig/lib:/mnt/storage/home/tk19812/scratch/software/SuiteSparse/lib:/mnt/storage/home/tk19812/scratch/software/libuv-v1.37.0/.libs:/mnt/storage/home/tk19812/scratch/software/nghttp2-1.40.0/lib/.libs:/mnt/storage/home/tk19812/scratch/software/openldap/libraries/liblmdb:/mnt/storage/home/tk19812/scratch/CIRCOS/circos-0.69-9/libgd-2.3.0/lib:/mnt/storage/home/tk19812/scratch/software/jemalloc/lib:/mnt/storage/home/tk19812/.conda/envs/test3k/lib:/mnt/storage/home/tk19812/scratch/software/portcullis/lib/python3.7/site-packages:/mnt/storage/home/tk19812/scratch/software/portcullis/boost_1_67_0/stage/lib:/mnt/storage/home/tk19812/scratch/software/cactus/lib:no/lib -Wl,--as-needed -static -L../kyotocabinet -L/mnt/storage/home/tk19812/scratch/software/lzo-2.10/lib -L. -L/mnt/storage/home/tk19812/scratch/software/cactus/lib -L/usr/local/lib -L/mnt/storage/home/tk19812/scratch/software/cactus/lib -Lno/lib -Wl,-rpath-link,.:/usr/local/lib:.:/usr/local/lib:/mnt/storage/easybuild/software/HDF5/1.8.17-foss-2016b/lib:/mnt/storage/easybuild/software/Szip/2.1-foss-2016b/lib:/mnt/storage/easybuild/software/zlib/1.2.8-foss-2016b/lib:/mnt/storage/easybuild/software/ScaLAPACK/2.0.2-gompi-2016b-OpenBLAS-0.2.18-LAPACK-3.6.1/lib:/mnt/storage/easybuild/software/OpenBLAS/0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.1/lib:/mnt/storage/easybuild/software/FFTW/3.3.4-gompi-2016b/lib:/mnt/storage/easybuild/software/OpenMPI/1.10.3-GCC-5.4.0-2.26/lib:/mnt/storage/easybuild/software/hwloc/1.11.3-GCC-5.4.0-2.26/lib:/mnt/storage/easybuild/software/numactl/2.0.11-GCC-5.4.0-2.26/lib:/mnt/storage/easybuild/software/binutils/2.26-GCCcore-5.4.0/lib:/mnt/storage/easybuild/software/GCCcore/5.4.0/lib/gcc/x86_64-unknown-linux-gnu/5.4.0:/mnt/storage/easybuild/software/GCCcore/5.4.0/lib64:/mnt/storage/easybuild/software/GCCcore/5.4.0/lib:/mnt/storage/software/apps/ncbi-blast/gnu/2.7.1/lib:/mnt/storage/easybuild/software/R/3.2.3-foss-2016a/lib64/R/lib:/mnt/storage/easybuild/software/R/3.2.3-foss-2016a/lib64:/mnt/storage/easybuild/software/GMP/6.1.0-foss-2016a/lib:/mnt/storage/easybuild/software/PROJ/4.9.2-foss-2016a/lib:/mnt/storage/easybuild/software/GDAL/2.0.2-foss-2016a/lib:/mnt/storage/easybuild/software/expat/2.1.0-foss-2016a/lib:/mnt/storage/easybuild/software/netCDF/4.3.3.1-foss-2016a/lib64:/mnt/storage/easybuild/software/libxml2/2.9.3-foss-2016a/lib:/mnt/storage/easybuild/software/cURL/7.47.0-foss-2016a/lib:/mnt/storage/easybuild/software/Tk/8.6.4-foss-2016a-no-X11/lib:/mnt/storage/easybuild/software/Tcl/8.6.4-foss-2016a/lib:/mnt/storage/easybuild/software/Java/1.8.0_72/lib:/mnt/storage/easybuild/software/libjpeg-turbo/1.4.2-foss-2016a/lib:/mnt/storage/easybuild/software/libpng/1.6.21-foss-2016a/lib:/mnt/storage/easybuild/software/libreadline/6.3-foss-2016a/lib:/mnt/storage/easybuild/software/ncurses/6.0-foss-2016a/lib:/mnt/storage/easybuild/software/bzip2/1.0.6-foss-2016a/lib:/mnt/storage/easybuild/software/GSL/2.3-foss-2017a/lib:/mnt/storage/easybuild/software/SQLite/3.13.0-GCC-5.4.0-2.26/lib:/mnt/storage/home/tk19812/software/lpsolve-5.5.0.10i/lib:/mnt/storage/home/tk19812/scratch/software/sparsehash/include:/mnt/storage/home/tk19812/scratch/software/bamtools/usr/local/lib64:/mnt/storage/home/tk19812/scratch/software/lzo-2.10/lib:/mnt/storage/home/tk19812/scratch/software/WiggleTools/lib:/mnt/storage/home/tk19812/scratch/software/cactus/lua-5.1.5/lib:/mnt/storage/home/tk19812/scratch/software/lzo-2.10/lib:/mnt/storage/home/tk19812/scratch/software/kyoto/lib:/mnt/storage/home/tk19812/scratch/software/swig-4.0.1/Lib:/mnt/storage/home/tk19812/scratch/software/openssl-1.1.1d/lib:/mnt/storage/home/tk19812/scratch/software/libBigWig/lib:/mnt/storage/home/tk19812/scratch/software/SuiteSparse/lib:/mnt/storage/home/tk19812/scratch/software/libuv-v1.37.0/.libs:/mnt/storage/home/tk19812/scratch/software/nghttp2-1.40.0/lib/.libs:/mnt/storage/home/tk19812/scratch/software/openldap/libraries/liblmdb:/mnt/storage/home/tk19812/scratch/CIRCOS/circos-0.69-9/libgd-2.3.0/lib:/mnt/storage/home/tk19812/scratch/software/jemalloc/lib:/mnt/storage/home/tk19812/.conda/envs/test3k/lib:/mnt/storage/home/tk19812/scratch/software/portcullis/lib/python3.7/site-packages:/mnt/storage/home/tk19812/scratch/software/portcullis/boost_1_67_0/stage/lib:/mnt/storage/home/tk19812/scratch/software/cactus/lib:no/lib -Wl,--as-needed -lkyototycoon -lkyotocabinet -lkyotocabinet -llzma -llzo2 -lz -lstdc++ -lresolv -lnsl -ldl -lrt -lpthread -lm -lc  -lkyotocabinet -llzma -llzo2 -lz -lstdc++ -lresolv -lnsl -ldl -lrt -lpthread -lm -lc 
/mnt/storage/easybuild/software/binutils/2.26-GCCcore-5.4.0/bin/ld.gold: error: cannot find -llzma
/mnt/storage/easybuild/software/binutils/2.26-GCCcore-5.4.0/bin/ld.gold: error: cannot find -llzma
./libkyototycoon.a(ktsocket.o):ktsocket.cc:function kyototycoon::Socket::get_host_address(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&): warning: Using 'getaddrinfo' in statically linked applications requires at runtime the shared libraries from the glibc version used for linking
/lib/../lib64/libpthread.a(libpthread.o):function sem_open: warning: the use of `mktemp' is dangerous, better use `mkstemp'
collect2: error: ld returned 1 exit status
make[3]: *** [ktutiltest] Error 1
make[3]: *** Waiting for unfinished jobs....
/mnt/storage/easybuild/software/binutils/2.26-GCCcore-5.4.0/bin/ld.gold: error: cannot find -llzma
/mnt/storage/easybuild/software/binutils/2.26-GCCcore-5.4.0/bin/ld.gold: error: cannot find -llzma
/lib/../lib64/libpthread.a(libpthread.o):function sem_open: warning: the use of `mktemp' is dangerous, better use `mkstemp'
collect2: error: ld returned 1 exit status
make[3]: *** [kttimedtest] Error 1
/mnt/storage/easybuild/software/binutils/2.26-GCCcore-5.4.0/bin/ld.gold: error: cannot find -llzma
/mnt/storage/easybuild/software/binutils/2.26-GCCcore-5.4.0/bin/ld.gold: error: cannot find -llzma
./libkyototycoon.a(ktsocket.o):ktsocket.cc:function kyototycoon::Socket::get_host_address(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&): warning: Using 'getaddrinfo' in statically linked applications requires at runtime the shared libraries from the glibc version used for linking
/lib/../lib64/libpthread.a(libpthread.o):function sem_open: warning: the use of `mktemp' is dangerous, better use `mkstemp'
collect2: error: ld returned 1 exit status
make[3]: *** [ktutilmgr] Error 1
/mnt/storage/easybuild/software/binutils/2.26-GCCcore-5.4.0/bin/ld.gold: error: cannot find -llzma
/mnt/storage/easybuild/software/binutils/2.26-GCCcore-5.4.0/bin/ld.gold: error: cannot find -llzma
./libkyototycoon.a(ktsocket.o):ktsocket.cc:function kyototycoon::Socket::get_host_address(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&): warning: Using 'getaddrinfo' in statically linked applications requires at runtime the shared libraries from the glibc version used for linking
/lib/../lib64/libpthread.a(libpthread.o):function sem_open: warning: the use of `mktemp' is dangerous, better use `mkstemp'
collect2: error: ld returned 1 exit status
make[3]: *** [ktutilserv] Error 1
make[3]: Leaving directory `/mnt/storage/scratch/tk19812/software/cactus/submodules/kyoto/kyototycoon'
make[2]: *** [tycoon] Error 2
make[2]: Leaving directory `/mnt/storage/scratch/tk19812/software/cactus/submodules/kyoto'
make[1]: *** [suball.kyoto] Error 2
make[1]: Leaving directory `/mnt/storage/scratch/tk19812/software/cactus'
make: *** [all] Error 2

Any help? F

-- You are receiving this because you were mentioned. Reply to this email directly or view it on GitHub: https://github.com/ComparativeGenomicsToolkit/cactus/issues/103#issuecomment-667502330Hi Mark,

I'm trying to reinstall cactus, given you updates. But I'm having problems again:

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Ready to install.

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make[3]: Leaving directory /mnt/storage/scratch/tk19812/software/cactus/submodules/kyoto/kyotocabinet' grep -q '^CPPFLAGS.*-D_KCDEBUG' kyotocabinet/Makefile || make -j4 -C kyotocabinet strip make[3]: Entering directory/mnt/storage/scratch/tk19812/software/cactus/submodules/kyoto/kyotocabinet' make[3]: warning: -jN forced in submake: disabling jobserver mode. strip kcutiltest kcutilmgr kcprototest kcstashtest kccachetest kcgrasstest kchashtest kchashmgr kctreetest kctreemgr kcdirtest kcdirmgr kcforesttest kcforestmgr kcpolytest kcpolymgr kclangctest make[3]: Leaving directory /mnt/storage/scratch/tk19812/software/cactus/submodules/kyoto/kyotocabinet' make -j4 -C kyototycoon make[3]: Entering directory/mnt/storage/scratch/tk19812/software/cactus/submodules/kyoto/kyototycoon' make[3]: warning: -jN forced in submake: disabling jobserver mode. g++ -g -O2 -Wall -fPIC -fsigned-char -g0 -O2 -Wno-unused-but-set-variable -Wno-unused-but-set-parameter -o ktutiltest ktutiltest.o -L../kyotocabinet -L/mnt/storage/home/tk19812/scratch/software/lzo-2.10/lib -L. -L/mnt/storage/home/tk19812/scratch/software/cactus/lib -L/usr/local/lib -L/mnt/storage/home/tk19812/scratch/software/cactus/lib -Lno/lib -Wl,-rpath-link,.:/usr/local/lib:.:/usr/local/lib:/mnt/storage/easybuild/software/HDF5/1.8.17-foss-2016b/lib:/mnt/storage/easybuild/software/Szip/2.1-foss-2016b/lib:/mnt/storage/easybuild/software/zlib/1.2.8-foss-2016b/lib:/mnt/storage/easybuild/software/ScaLAPACK/2.0.2-gompi-2016b-OpenBLAS-0.2.18-LAPACK-3.6.1/lib:/mnt/storage/easybuild/software/OpenBLAS/0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.1/lib:/mnt/storage/easybuild/software/FFTW/3.3.4-gompi-2016b/lib:/mnt/storage/easybuild/software/OpenMPI/1.10.3-GCC-5.4.0-2.26/lib:/mnt/storage/easybuild/software/hwloc/1.11.3-GCC-5.4.0-2.26/lib:/mnt/storage/easybuild/software/numactl/2.0.11-GCC-5.4.0-2.26/lib:/mnt/storage/easybuild/software/binutils/2.26-GCCcore-5.4.0/lib:/mnt/storage/easybuild/software/GCCcore/5.4.0/lib/gcc/x86_64-unknown-linux-gnu/5.4.0:/mnt/storage/easybuild/software/GCCcore/5.4.0/lib64:/mnt/storage/easybuild/software/GCCcore/5.4.0/lib:/mnt/storage/software/apps/ncbi-blast/gnu/2.7.1/lib:/mnt/storage/easybuild/software/R/3.2.3-foss-2016a/lib64/R/lib:/mnt/storage/easybuild/software/R/3.2.3-foss-2016a/lib64:/mnt/storage/easybuild/software/GMP/6.1.0-foss-2016a/lib:/mnt/storage/easybuild/software/PROJ/4.9.2-foss-2016a/lib:/mnt/storage/easybuild/software/GDAL/2.0.2-foss-2016a/lib:/mnt/storage/easybuild/software/expat/2.1.0-foss-2016a/lib:/mnt/storage/easybuild/software/netCDF/4.3.3.1-foss-2016a/lib64:/mnt/storage/easybuild/software/libxml2/2.9.3-foss-2016a/lib:/mnt/storage/easybuild/software/cURL/7.47.0-foss-2016a/lib:/mnt/storage/easybuild/software/Tk/8.6.4-foss-2016a-no-X11/lib:/mnt/storage/easybuild/software/Tcl/8.6.4-foss-2016a/lib:/mnt/storage/easybuild/software/Java/1.8.0_72/lib:/mnt/storage/easybuild/software/libjpeg-turbo/1.4.2-foss-2016a/lib:/mnt/storage/easybuild/software/libpng/1.6.21-foss-2016a/lib:/mnt/storage/easybuild/software/libreadline/6.3-foss-2016a/lib:/mnt/storage/easybuild/software/ncurses/6.0-foss-2016a/lib:/mnt/storage/easybuild/software/bzip2/1.0.6-foss-2016a/lib:/mnt/storage/easybuild/software/GSL/2.3-foss-2017a/lib:/mnt/storage/easybuild/software/SQLite/3.13.0-GCC-5.4.0-2.26/lib:/mnt/storage/home/tk19812/software/lpsolve-5.5.0.10i/lib:/mnt/storage/home/tk19812/scratch/software/sparsehash/include:/mnt/storage/home/tk19812/scratch/software/bamtools/usr/local/lib64:/mnt/storage/home/tk19812/scratch/software/lzo-2.10/lib:/mnt/storage/home/tk19812/scratch/software/WiggleTools/lib:/mnt/storage/home/tk19812/scratch/software/cactus/lua-5.1.5/lib:/mnt/storage/home/tk19812/scratch/software/lzo-2.10/lib:/mnt/storage/home/tk19812/scratch/software/kyoto/lib:/mnt/storage/home/tk19812/scratch/software/swig-4.0.1/Lib:/mnt/storage/home/tk19812/scratch/software/openssl-1.1.1d/lib:/mnt/storage/home/tk19812/scratch/software/libBigWig/lib:/mnt/storage/home/tk19812/scratch/software/SuiteSparse/lib:/mnt/storage/home/tk19812/scratch/software/libuv-v1.37.0/.libs:/mnt/storage/home/tk19812/scratch/software/nghttp2-1.40.0/lib/.libs:/mnt/storage/home/tk19812/scratch/software/openldap/libraries/liblmdb:/mnt/storage/home/tk19812/scratch/CIRCOS/circos-0.69-9/libgd-2.3.0/lib:/mnt/storage/home/tk19812/scratch/software/jemalloc/lib:/mnt/storage/home/tk19812/.conda/envs/test3k/lib:/mnt/storage/home/tk19812/scratch/software/portcullis/lib/python3.7/site-packages:/mnt/storage/home/tk19812/scratch/software/portcullis/boost_1_67_0/stage/lib:/mnt/storage/home/tk19812/scratch/software/cactus/lib:no/lib -Wl,--as-needed -static -L../kyotocabinet -L/mnt/storage/home/tk19812/scratch/software/lzo-2.10/lib -L. -L/mnt/storage/home/tk19812/scratch/software/cactus/lib -L/usr/local/lib -L/mnt/storage/home/tk19812/scratch/software/cactus/lib -Lno/lib -Wl,-rpath-link,.:/usr/local/lib:.:/usr/local/lib:/mnt/storage/easybuild/software/HDF5/1.8.17-foss-2016b/lib:/mnt/storage/easybuild/software/Szip/2.1-foss-2016b/lib:/mnt/storage/easybuild/software/zlib/1.2.8-foss-2016b/lib:/mnt/storage/easybuild/software/ScaLAPACK/2.0.2-gompi-2016b-OpenBLAS-0.2.18-LAPACK-3.6.1/lib:/mnt/storage/easybuild/software/OpenBLAS/0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.1/lib:/mnt/storage/easybuild/software/FFTW/3.3.4-gompi-2016b/lib:/mnt/storage/easybuild/software/OpenMPI/1.10.3-GCC-5.4.0-2.26/lib:/mnt/storage/easybuild/software/hwloc/1.11.3-GCC-5.4.0-2.26/lib:/mnt/storage/easybuild/software/numactl/2.0.11-GCC-5.4.0-2.26/lib:/mnt/storage/easybuild/software/binutils/2.26-GCCcore-5.4.0/lib:/mnt/storage/easybuild/software/GCCcore/5.4.0/lib/gcc/x86_64-unknown-linux-gnu/5.4.0:/mnt/storage/easybuild/software/GCCcore/5.4.0/lib64:/mnt/storage/easybuild/software/GCCcore/5.4.0/lib:/mnt/storage/software/apps/ncbi-blast/gnu/2.7.1/lib:/mnt/storage/easybuild/software/R/3.2.3-foss-2016a/lib64/R/lib:/mnt/storage/easybuild/software/R/3.2.3-foss-2016a/lib64:/mnt/storage/easybuild/software/GMP/6.1.0-foss-2016a/lib:/mnt/storage/easybuild/software/PROJ/4.9.2-foss-2016a/lib:/mnt/storage/easybuild/software/GDAL/2.0.2-foss-2016a/lib:/mnt/storage/easybuild/software/expat/2.1.0-foss-2016a/lib:/mnt/storage/easybuild/software/netCDF/4.3.3.1-foss-2016a/lib64:/mnt/storage/easybuild/software/libxml2/2.9.3-foss-2016a/lib:/mnt/storage/easybuild/software/cURL/7.47.0-foss-2016a/lib:/mnt/storage/easybuild/software/Tk/8.6.4-foss-2016a-no-X11/lib:/mnt/storage/easybuild/software/Tcl/8.6.4-foss-2016a/lib:/mnt/storage/easybuild/software/Java/1.8.0_72/lib:/mnt/storage/easybuild/software/libjpeg-turbo/1.4.2-foss-2016a/lib:/mnt/storage/easybuild/software/libpng/1.6.21-foss-2016a/lib:/mnt/storage/easybuild/software/libreadline/6.3-foss-2016a/lib:/mnt/storage/easybuild/software/ncurses/6.0-foss-2016a/lib:/mnt/storage/easybuild/software/bzip2/1.0.6-foss-2016a/lib:/mnt/storage/easybuild/software/GSL/2.3-foss-2017a/lib:/mnt/storage/easybuild/software/SQLite/3.13.0-GCC-5.4.0-2.26/lib:/mnt/storage/home/tk19812/software/lpsolve-5.5.0.10i/lib:/mnt/storage/home/tk19812/scratch/software/sparsehash/include:/mnt/storage/home/tk19812/scratch/software/bamtools/usr/local/lib64:/mnt/storage/home/tk19812/scratch/software/lzo-2.10/lib:/mnt/storage/home/tk19812/scratch/software/WiggleTools/lib:/mnt/storage/home/tk19812/scratch/software/cactus/lua-5.1.5/lib:/mnt/storage/home/tk19812/scratch/software/lzo-2.10/lib:/mnt/storage/home/tk19812/scratch/software/kyoto/lib:/mnt/storage/home/tk19812/scratch/software/swig-4.0.1/Lib:/mnt/storage/home/tk19812/scratch/software/openssl-1.1.1d/lib:/mnt/storage/home/tk19812/scratch/software/libBigWig/lib:/mnt/storage/home/tk19812/scratch/software/SuiteSparse/lib:/mnt/storage/home/tk19812/scratch/software/libuv-v1.37.0/.libs:/mnt/storage/home/tk19812/scratch/software/nghttp2-1.40.0/lib/.libs:/mnt/storage/home/tk19812/scratch/software/openldap/libraries/liblmdb:/mnt/storage/home/tk19812/scratch/CIRCOS/circos-0.69-9/libgd-2.3.0/lib:/mnt/storage/home/tk19812/scratch/software/jemalloc/lib:/mnt/storage/home/tk19812/.conda/envs/test3k/lib:/mnt/storage/home/tk19812/scratch/software/portcullis/lib/python3.7/site-packages:/mnt/storage/home/tk19812/scratch/software/portcullis/boost_1_67_0/stage/lib:/mnt/storage/home/tk19812/scratch/software/cactus/lib:no/lib -Wl,--as-needed -lkyototycoon -lkyotocabinet -lkyotocabinet -llzma -llzo2 -lz -lstdc++ -lresolv -lnsl -ldl -lrt -lpthread -lm -lc -lkyotocabinet -llzma -llzo2 -lz -lstdc++ -lresolv -lnsl -ldl -lrt -lpthread -lm -lc g++ -g -O2 -Wall -fPIC -fsigned-char -g0 -O2 -Wno-unused-but-set-variable -Wno-unused-but-set-parameter -o ktutilmgr ktutilmgr.o -L../kyotocabinet -L/mnt/storage/home/tk19812/scratch/software/lzo-2.10/lib -L. -L/mnt/storage/home/tk19812/scratch/software/cactus/lib -L/usr/local/lib -L/mnt/storage/home/tk19812/scratch/software/cactus/lib -Lno/lib -Wl,-rpath-link,.:/usr/local/lib:.:/usr/local/lib:/mnt/storage/easybuild/software/HDF5/1.8.17-foss-2016b/lib:/mnt/storage/easybuild/software/Szip/2.1-foss-2016b/lib:/mnt/storage/easybuild/software/zlib/1.2.8-foss-2016b/lib:/mnt/storage/easybuild/software/ScaLAPACK/2.0.2-gompi-2016b-OpenBLAS-0.2.18-LAPACK-3.6.1/lib:/mnt/storage/easybuild/software/OpenBLAS/0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.1/lib:/mnt/storage/easybuild/software/FFTW/3.3.4-gompi-2016b/lib:/mnt/storage/easybuild/software/OpenMPI/1.10.3-GCC-5.4.0-2.26/lib:/mnt/storage/easybuild/software/hwloc/1.11.3-GCC-5.4.0-2.26/lib:/mnt/storage/easybuild/software/numactl/2.0.11-GCC-5.4.0-2.26/lib:/mnt/storage/easybuild/software/binutils/2.26-GCCcore-5.4.0/lib:/mnt/storage/easybuild/software/GCCcore/5.4.0/lib/gcc/x86_64-unknown-linux-gnu/5.4.0:/mnt/storage/easybuild/software/GCCcore/5.4.0/lib64:/mnt/storage/easybuild/software/GCCcore/5.4.0/lib:/mnt/storage/software/apps/ncbi-blast/gnu/2.7.1/lib:/mnt/storage/easybuild/software/R/3.2.3-foss-2016a/lib64/R/lib:/mnt/storage/easybuild/software/R/3.2.3-foss-2016a/lib64:/mnt/storage/easybuild/software/GMP/6.1.0-foss-2016a/lib:/mnt/storage/easybuild/software/PROJ/4.9.2-foss-2016a/lib:/mnt/storage/easybuild/software/GDAL/2.0.2-foss-2016a/lib:/mnt/storage/easybuild/software/expat/2.1.0-foss-2016a/lib:/mnt/storage/easybuild/software/netCDF/4.3.3.1-foss-2016a/lib64:/mnt/storage/easybuild/software/libxml2/2.9.3-foss-2016a/lib:/mnt/storage/easybuild/software/cURL/7.47.0-foss-2016a/lib:/mnt/storage/easybuild/software/Tk/8.6.4-foss-2016a-no-X11/lib:/mnt/storage/easybuild/software/Tcl/8.6.4-foss-2016a/lib:/mnt/storage/easybuild/software/Java/1.8.0_72/lib:/mnt/storage/easybuild/software/libjpeg-turbo/1.4.2-foss-2016a/lib:/mnt/storage/easybuild/software/libpng/1.6.21-foss-2016a/lib:/mnt/storage/easybuild/software/libreadline/6.3-foss-2016a/lib:/mnt/storage/easybuild/software/ncurses/6.0-foss-2016a/lib:/mnt/storage/easybuild/software/bzip2/1.0.6-foss-2016a/lib:/mnt/storage/easybuild/software/GSL/2.3-foss-2017a/lib:/mnt/storage/easybuild/software/SQLite/3.13.0-GCC-5.4.0-2.26/lib:/mnt/storage/home/tk19812/software/lpsolve-5.5.0.10i/lib:/mnt/storage/home/tk19812/scratch/software/sparsehash/include:/mnt/storage/home/tk19812/scratch/software/bamtools/usr/local/lib64:/mnt/storage/home/tk19812/scratch/software/lzo-2.10/lib:/mnt/storage/home/tk19812/scratch/software/WiggleTools/lib:/mnt/storage/home/tk19812/scratch/software/cactus/lua-5.1.5/lib:/mnt/storage/home/tk19812/scratch/software/lzo-2.10/lib:/mnt/storage/home/tk19812/scratch/software/kyoto/lib:/mnt/storage/home/tk19812/scratch/software/swig-4.0.1/Lib:/mnt/storage/home/tk19812/scratch/software/openssl-1.1.1d/lib:/mnt/storage/home/tk19812/scratch/software/libBigWig/lib:/mnt/storage/home/tk19812/scratch/software/SuiteSparse/lib:/mnt/storage/home/tk19812/scratch/software/libuv-v1.37.0/.libs:/mnt/storage/home/tk19812/scratch/software/nghttp2-1.40.0/lib/.libs:/mnt/storage/home/tk19812/scratch/software/openldap/libraries/liblmdb:/mnt/storage/home/tk19812/scratch/CIRCOS/circos-0.69-9/libgd-2.3.0/lib:/mnt/storage/home/tk19812/scratch/software/jemalloc/lib:/mnt/storage/home/tk19812/.conda/envs/test3k/lib:/mnt/storage/home/tk19812/scratch/software/portcullis/lib/python3.7/site-packages:/mnt/storage/home/tk19812/scratch/software/portcullis/boost_1_67_0/stage/lib:/mnt/storage/home/tk19812/scratch/software/cactus/lib:no/lib -Wl,--as-needed -static -L../kyotocabinet -L/mnt/storage/home/tk19812/scratch/software/lzo-2.10/lib -L. -L/mnt/storage/home/tk19812/scratch/software/cactus/lib -L/usr/local/lib -L/mnt/storage/home/tk19812/scratch/software/cactus/lib -Lno/lib -Wl,-rpath-link,.:/usr/local/lib:.:/usr/local/lib:/mnt/storage/easybuild/software/HDF5/1.8.17-foss-2016b/lib:/mnt/storage/easybuild/software/Szip/2.1-foss-2016b/lib:/mnt/storage/easybuild/software/zlib/1.2.8-foss-2016b/lib:/mnt/storage/easybuild/software/ScaLAPACK/2.0.2-gompi-2016b-OpenBLAS-0.2.18-LAPACK-3.6.1/lib:/mnt/storage/easybuild/software/OpenBLAS/0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.1/lib:/mnt/storage/easybuild/software/FFTW/3.3.4-gompi-2016b/lib:/mnt/storage/easybuild/software/OpenMPI/1.10.3-GCC-5.4.0-2.26/lib:/mnt/storage/easybuild/software/hwloc/1.11.3-GCC-5.4.0-2.26/lib:/mnt/storage/easybuild/software/numactl/2.0.11-GCC-5.4.0-2.26/lib:/mnt/storage/easybuild/software/binutils/2.26-GCCcore-5.4.0/lib:/mnt/storage/easybuild/software/GCCcore/5.4.0/lib/gcc/x86_64-unknown-linux-gnu/5.4.0:/mnt/storage/easybuild/software/GCCcore/5.4.0/lib64:/mnt/storage/easybuild/software/GCCcore/5.4.0/lib:/mnt/storage/software/apps/ncbi-blast/gnu/2.7.1/lib:/mnt/storage/easybuild/software/R/3.2.3-foss-2016a/lib64/R/lib:/mnt/storage/easybuild/software/R/3.2.3-foss-2016a/lib64:/mnt/storage/easybuild/software/GMP/6.1.0-foss-2016a/lib:/mnt/storage/easybuild/software/PROJ/4.9.2-foss-2016a/lib:/mnt/storage/easybuild/software/GDAL/2.0.2-foss-2016a/lib:/mnt/storage/easybuild/software/expat/2.1.0-foss-2016a/lib:/mnt/storage/easybuild/software/netCDF/4.3.3.1-foss-2016a/lib64:/mnt/storage/easybuild/software/libxml2/2.9.3-foss-2016a/lib:/mnt/storage/easybuild/software/cURL/7.47.0-foss-2016a/lib:/mnt/storage/easybuild/software/Tk/8.6.4-foss-2016a-no-X11/lib:/mnt/storage/easybuild/software/Tcl/8.6.4-foss-2016a/lib:/mnt/storage/easybuild/software/Java/1.8.0_72/lib:/mnt/storage/easybuild/software/libjpeg-turbo/1.4.2-foss-2016a/lib:/mnt/storage/easybuild/software/libpng/1.6.21-foss-2016a/lib:/mnt/storage/easybuild/software/libreadline/6.3-foss-2016a/lib:/mnt/storage/easybuild/software/ncurses/6.0-foss-2016a/lib:/mnt/storage/easybuild/software/bzip2/1.0.6-foss-2016a/lib:/mnt/storage/easybuild/software/GSL/2.3-foss-2017a/lib:/mnt/storage/easybuild/software/SQLite/3.13.0-GCC-5.4.0-2.26/lib:/mnt/storage/home/tk19812/software/lpsolve-5.5.0.10i/lib:/mnt/storage/home/tk19812/scratch/software/sparsehash/include:/mnt/storage/home/tk19812/scratch/software/bamtools/usr/local/lib64:/mnt/storage/home/tk19812/scratch/software/lzo-2.10/lib:/mnt/storage/home/tk19812/scratch/software/WiggleTools/lib:/mnt/storage/home/tk19812/scratch/software/cactus/lua-5.1.5/lib:/mnt/storage/home/tk19812/scratch/software/lzo-2.10/lib:/mnt/storage/home/tk19812/scratch/software/kyoto/lib:/mnt/storage/home/tk19812/scratch/software/swig-4.0.1/Lib:/mnt/storage/home/tk19812/scratch/software/openssl-1.1.1d/lib:/mnt/storage/home/tk19812/scratch/software/libBigWig/lib:/mnt/storage/home/tk19812/scratch/software/SuiteSparse/lib:/mnt/storage/home/tk19812/scratch/software/libuv-v1.37.0/.libs:/mnt/storage/home/tk19812/scratch/software/nghttp2-1.40.0/lib/.libs:/mnt/storage/home/tk19812/scratch/software/openldap/libraries/liblmdb:/mnt/storage/home/tk19812/scratch/CIRCOS/circos-0.69-9/libgd-2.3.0/lib:/mnt/storage/home/tk19812/scratch/software/jemalloc/lib:/mnt/storage/home/tk19812/.conda/envs/test3k/lib:/mnt/storage/home/tk19812/scratch/software/portcullis/lib/python3.7/site-packages:/mnt/storage/home/tk19812/scratch/software/portcullis/boost_1_67_0/stage/lib:/mnt/storage/home/tk19812/scratch/software/cactus/lib:no/lib -Wl,--as-needed -lkyototycoon -lkyotocabinet -lkyotocabinet -llzma -llzo2 -lz -lstdc++ -lresolv -lnsl -ldl -lrt -lpthread -lm -lc -lkyotocabinet -llzma -llzo2 -lz -lstdc++ -lresolv -lnsl -ldl -lrt -lpthread -lm -lc g++ -g -O2 -Wall -fPIC -fsigned-char -g0 -O2 -Wno-unused-but-set-variable -Wno-unused-but-set-parameter -o ktutilserv ktutilserv.o -L../kyotocabinet -L/mnt/storage/home/tk19812/scratch/software/lzo-2.10/lib -L. -L/mnt/storage/home/tk19812/scratch/software/cactus/lib -L/usr/local/lib -L/mnt/storage/home/tk19812/scratch/software/cactus/lib -Lno/lib 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-Wl,--as-needed -static -L../kyotocabinet -L/mnt/storage/home/tk19812/scratch/software/lzo-2.10/lib -L. -L/mnt/storage/home/tk19812/scratch/software/cactus/lib -L/usr/local/lib -L/mnt/storage/home/tk19812/scratch/software/cactus/lib -Lno/lib 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[francicco]

Hi Mark,

the example job finishes with this, which seems to be an error:

bc4login3.bc4.acrc.priv 2020-08-02 08:26:45,257 MainThread INFO toil.leader: Failed jobs at end of the run: 'RunCactusPreprocessorThenProgressiveDown2' kind-RunCactusPreprocessorThenProgressiveDown2/instance-9mdzphzt 'RunCactusPreprocessorThenProgressiveDown' kind-RunCactusPreprocessorThenProgressiveDown/instance-x8gh8yet 'exportHal' kind-exportHal/instance-v5p_84oy
Workflow Progress 100%|███████████████████████████████████████████████████████████████████████████████████████████████████████████| 1049/1049 (0 failures) [39:52<00:00, 0.44 jobs/s]
bc4login3.bc4.acrc.priv 2020-08-02 08:26:45,258 MainThread INFO toil.realtimeLogger: Stopping real-time logging server.
bc4login3.bc4.acrc.priv 2020-08-02 08:26:45,288 MainThread INFO toil.realtimeLogger: Joining real-time logging server thread.
Traceback (most recent call last):
  File "/mnt/storage/scratch/tk19812/software/cactus-bin-v1.1.1/venv/bin/cactus", line 8, in <module>
    sys.exit(main())
  File "/mnt/storage/scratch/tk19812/software/cactus-bin-v1.1.1/venv/lib/python3.7/site-packages/cactus/progressive/cactus_progressive.py", line 406, in main
    runCactusProgressive(options)
  File "/mnt/storage/scratch/tk19812/software/cactus-bin-v1.1.1/venv/lib/python3.7/site-packages/cactus/progressive/cactus_progressive.py", line 454, in runCactusProgressive
    halID = toil.start(RunCactusPreprocessorThenProgressiveDown(options, project, memory=configWrapper.getDefaultMemory()))
  File "/mnt/storage/scratch/tk19812/software/cactus-bin-v1.1.1/venv/lib/python3.7/site-packages/toil/common.py", line 829, in start
    return self._runMainLoop(rootJobGraph)
  File "/mnt/storage/scratch/tk19812/software/cactus-bin-v1.1.1/venv/lib/python3.7/site-packages/toil/common.py", line 1120, in _runMainLoop
    jobCache=self._jobCache).run()
  File "/mnt/storage/scratch/tk19812/software/cactus-bin-v1.1.1/venv/lib/python3.7/site-packages/toil/leader.py", line 269, in run
    raise FailedJobsException(self.config.jobStore, self.toilState.totalFailedJobs, self.jobStore)
toil.leader.FailedJobsException: The job store 'file:/mnt/storage/scratch/tk19812/software/cactus-bin-v1.1.1/jobstore' contains 3 failed jobs: 'RunCactusPreprocessorThenProgressiveDown2' kind-RunCactusPreprocessorThenProgressiveDown2/instance-9mdzphzt, 'RunCactusPreprocessorThenProgressiveDown' kind-RunCactusPreprocessorThenProgressiveDown/instance-x8gh8yet, 'exportHal' kind-exportHal/instance-v5p_84oy
Log from job 'exportHal' kind-exportHal/instance-v5p_84oy follows:
=========>
    INFO:toil.worker:---TOIL WORKER OUTPUT LOG---
    INFO:toil:Running Toil version 4.1.0-5ad5e77d98e1456b4f70f5b00e688a43cdce2ebe.
    INFO:cactus.shared.common:Running the command ['halAppendCactusSubtree', 'tmpipdfryn9.tmp', 'tmp4daqtaw_.tmp', '(Anc1:0.020593,Anc2:0.032898)Anc0;', 'tmp_alignment.hal']
    INFO:toil-rt:2020-08-02 08:26:32.600335: Running the command: "halAppendCactusSubtree tmpipdfryn9.tmp tmp4daqtaw_.tmp (Anc1:0.020593,Anc2:0.032898)Anc0; tmp_alignment.hal"
    INFO:toil-rt:2020-08-02 08:26:32.821252: Successfully ran the command: "halAppendCactusSubtree tmpipdfryn9.tmp tmp4daqtaw_.tmp (Anc1:0.020593,Anc2:0.032898)Anc0; tmp_alignment.hal" in 0.21368145942687988 seconds
    INFO:cactus.shared.common:Running the command ['halAppendCactusSubtree', 'tmpvqx5_zaj.tmp', 'tmpjg2pohn9.tmp', '(simHuman_chr6:0.144018,mr:0.271974)Anc1;', 'tmp_alignment.hal', '--outgroups', 'Anc2']
    INFO:toil-rt:2020-08-02 08:26:32.832903: Running the command: "halAppendCactusSubtree tmpvqx5_zaj.tmp tmpjg2pohn9.tmp (simHuman_chr6:0.144018,mr:0.271974)Anc1; tmp_alignment.hal --outgroups Anc2"
    INFO:toil-rt:2020-08-02 08:26:34.354915: Successfully ran the command: "halAppendCactusSubtree tmpvqx5_zaj.tmp tmpjg2pohn9.tmp (simHuman_chr6:0.144018,mr:0.271974)Anc1; tmp_alignment.hal --outgroups Anc2" in 1.5150477886199951 seconds
    INFO:cactus.shared.common:Running the command ['halAppendCactusSubtree', 'tmp420400hr.tmp', 'tmprtp1iitl.tmp', '(simCow_chr6:0.18908,simDog_chr6:0.16303)Anc2;', 'tmp_alignment.hal', '--outgroups', 'simHuman_chr6,simMouse_chr6,simRat_chr6']
    INFO:toil-rt:2020-08-02 08:26:34.368783: Running the command: "halAppendCactusSubtree tmp420400hr.tmp tmprtp1iitl.tmp (simCow_chr6:0.18908,simDog_chr6:0.16303)Anc2; tmp_alignment.hal --outgroups simHuman_chr6,simMouse_chr6,simRat_chr6"
    INFO:toil-rt:2020-08-02 08:26:35.991579: Successfully ran the command: "halAppendCactusSubtree tmp420400hr.tmp tmprtp1iitl.tmp (simCow_chr6:0.18908,simDog_chr6:0.16303)Anc2; tmp_alignment.hal --outgroups simHuman_chr6,simMouse_chr6,simRat_chr6" in 1.6151318550109863 seconds
    INFO:cactus.shared.common:Running the command ['halAppendCactusSubtree', 'tmpjfjz92vy.tmp', 'tmpkz_wzhdt.tmp', '(simMouse_chr6:0.084509,simRat_chr6:0.091589)mr;', 'tmp_alignment.hal', '--outgroups', 'simHuman_chr6,simDog_chr6,simCow_chr6']
    INFO:toil-rt:2020-08-02 08:26:36.004648: Running the command: "halAppendCactusSubtree tmpjfjz92vy.tmp tmpkz_wzhdt.tmp (simMouse_chr6:0.084509,simRat_chr6:0.091589)mr; tmp_alignment.hal --outgroups simHuman_chr6,simDog_chr6,simCow_chr6"
    INFO:toil-rt:2020-08-02 08:26:36.776133: Successfully ran the command: "halAppendCactusSubtree tmpjfjz92vy.tmp tmpkz_wzhdt.tmp (simMouse_chr6:0.084509,simRat_chr6:0.091589)mr; tmp_alignment.hal --outgroups simHuman_chr6,simDog_chr6,simCow_chr6" in 0.7642290592193604 seconds
    INFO:cactus.shared.common:Running the command ['halSetMetadata', 'tmp_alignment.hal', 'CACTUS_COMMIT', 'c087fe129d8c337c7eab961cebd49c80bcc20ef3']
    INFO:toil-rt:2020-08-02 08:26:36.776737: Running the command: "halSetMetadata tmp_alignment.hal CACTUS_COMMIT c087fe129d8c337c7eab961cebd49c80bcc20ef3"
    HDF5-DIAG: Error detected in HDF5 (1.8.16) thread 0:
      #000: H5A.c line 249 in H5Acreate2(): no write intent on file
        major: Invalid arguments to routine
        minor: Write failed
    terminate called after throwing an instance of 'H5::AttributeIException'
    Traceback (most recent call last):
      File "/mnt/storage/scratch/tk19812/software/cactus-bin-v1.1.1/venv/lib/python3.7/site-packages/toil/worker.py", line 366, in workerScript
        job._runner(jobGraph=jobGraph, jobStore=jobStore, fileStore=fileStore, defer=defer)
      File "/mnt/storage/scratch/tk19812/software/cactus-bin-v1.1.1/venv/lib/python3.7/site-packages/toil/job.py", line 1392, in _runner
        returnValues = self._run(jobGraph, fileStore)
      File "/mnt/storage/scratch/tk19812/software/cactus-bin-v1.1.1/venv/lib/python3.7/site-packages/toil/job.py", line 1329, in _run
        return self.run(fileStore)
      File "/mnt/storage/scratch/tk19812/software/cactus-bin-v1.1.1/venv/lib/python3.7/site-packages/toil/job.py", line 1533, in run
        rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs)
      File "/mnt/storage/scratch/tk19812/software/cactus-bin-v1.1.1/venv/lib/python3.7/site-packages/cactus/progressive/cactus_progressive.py", line 332, in exportHal
        cactus_call(parameters=["halSetMetadata", HALPath, "CACTUS_COMMIT", cactus_commit])
      File "/mnt/storage/scratch/tk19812/software/cactus-bin-v1.1.1/venv/lib/python3.7/site-packages/cactus/shared/common.py", line 1281, in cactus_call
        raise RuntimeError("Command {} signaled {}: {}".format(call, signal.Signals(-process.returncode).name, out))
    RuntimeError: Command ['halSetMetadata', 'tmp_alignment.hal', 'CACTUS_COMMIT', 'c087fe129d8c337c7eab961cebd49c80bcc20ef3'] signaled SIGABRT: stdout=None
    ERROR:toil.worker:Exiting the worker because of a failed job on host bc4login3.bc4.acrc.priv
    WARNING:toil.jobGraph:Due to failure we are reducing the remaining retry count of job 'exportHal' kind-exportHal/instance-v5p_84oy with ID kind-exportHal/instance-v5p_84oy to 0
<=========

F

[diekhans]

I have never see thus error before

HDF5-DIAG: Error detected in HDF5 (1.8.16) thread 0:
  #000: H5A.c line 249 in H5Acreate2(): no write intent on file
    major: Invalid arguments to routine
    minor: Write failed
terminate called after throwing an instance of 'H5::AttributeIException'

try running

make test

in the submodules/hal/api directory

[francicco]

The only subfolder in submodules directory is sonLib. I guess a lot of stuff is missing. F

[diekhans]

ah, you have hal, not the full cactus tree.

Just run the hal/api tests and see if they pass.

Francesco Cicconardi notifications@github.com writes:

The only subfolder in submodules directory is sonLib. I guess a lot of stuff is missing. F

-- You are receiving this because you were mentioned. Reply to this email directly or view it on GitHub: https://github.com/ComparativeGenomicsToolkit/cactus/issues/103#issuecomment-667702163 The only subfolder in submodules directory is sonLib. I guess a lot of stuff is missing. F

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or unsubscribe.*

[francicco]

(venv) [tk19812@bc4login3 api]$ make test
../bin/halHdf5Tests

OK (0 tests)

../bin/halApiTests hdf5
Running test case halAlignmentTestTrees
Running test case halGenomeMetaTest
Running test case halGenomeCreateTest
Running test case halGenomeUpdateTest
Running test case halGenomeStringTest
Running test case halGenomeCopyTest
Running test case halGenomeCopySegmentsWhenSequencesOutOfOrderTest
Running test case halGenomeDNAPackUnpackTest
Running test case halTopSegmentSimpleIteratorTest
Running test case halTopSegmentSequenceTest
Running test case halTopSegmentIteratorParseTest
Running test case halTopSegmentIteratorToSiteTest
Running test case halTopSegmentIteratorReverseTest
Running test case halTopSegmentIsGapTest
Running test case halBottomSegmentSimpleIteratorTest
Running test case halBottomSegmentSequenceTest
Running test case halBottomSegmentIteratorParseTest
Running test case halBottomSegmentIteratorToSiteTest
Running test case halBottomSegmentIteratorReverseTest
Running test case halBottomSegmentIsGapTest
Running test case halSequenceCreateTest
Running test case halSequenceIteratorTest
Running test case halSequenceUpdateTest
Running test case halSequenceRenameTest
Running test case halColumnIteratorBaseTest
Running test case halColumnIteratorDepthTest
Running test case halColumnIteratorDupTest
Running test case halColumnIteratorInvTest
Running test case halColumnIteratorGapTest
Running test case halColumnIteratorMultiGapTest
Running test case halColumnIteratorMultiGapInvTest
Running test case halColumnIteratorPositionCacheTest
Running test case halGappedSegmentSimpleIteratorTest
Running test case halGappedSegmentSimpleIteratorTest2
Running test case halGappedSegmentIteratorIndelTest
Running test case halRearrangementInsertionTest
Running test case halRearrangementSimpleInversionTest
Running test case halRearrangementGappedInversionTest
Running test case halMappedSegmentMapExtraParalogsTest
Running test case halMappedSegmentMapUpTest
Running test case halMappedSegmentMapDownTest
Running test case halMappedSegmentParseTest
Running test case halMappedSegmentMapAcrossTest
Running test case halMappedSegmentMapDupeTest
Running test case halMappedSegmentColCompareTestCheck1
Running test case halMappedSegmentColCompareTestCheck2
Running test case halMappedSegmentColCompareTest1
Running test case halValidateSmallTest
Running test case halValidateMediumTest
Running test case halValidateManyGenomesTest
..................................................

OK (50 tests)

../bin/halApiTests mmap
Running test case halAlignmentTestTrees
Running test case halGenomeMetaTest
Running test case halGenomeCreateTest
Running test case halGenomeUpdateTest
Running test case halGenomeStringTest
Running test case halGenomeCopyTest
Running test case halGenomeCopySegmentsWhenSequencesOutOfOrderTest
Running test case halGenomeDNAPackUnpackTest
Running test case halTopSegmentSimpleIteratorTest
Running test case halTopSegmentSequenceTest
Running test case halTopSegmentIteratorParseTest
Running test case halTopSegmentIteratorToSiteTest
Running test case halTopSegmentIteratorReverseTest
Running test case halTopSegmentIsGapTest
Running test case halBottomSegmentSimpleIteratorTest
Running test case halBottomSegmentSequenceTest
Running test case halBottomSegmentIteratorParseTest
Running test case halBottomSegmentIteratorToSiteTest
Running test case halBottomSegmentIteratorReverseTest
Running test case halBottomSegmentIsGapTest
Running test case halSequenceCreateTest
Running test case halSequenceIteratorTest
Running test case halSequenceUpdateTest
Running test case halSequenceRenameTest
Running test case halColumnIteratorBaseTest
Running test case halColumnIteratorDepthTest
Running test case halColumnIteratorDupTest
Running test case halColumnIteratorInvTest
Running test case halColumnIteratorGapTest
Running test case halColumnIteratorMultiGapTest
Running test case halColumnIteratorMultiGapInvTest
Running test case halColumnIteratorPositionCacheTest
Running test case halGappedSegmentSimpleIteratorTest
Running test case halGappedSegmentSimpleIteratorTest2
Running test case halGappedSegmentIteratorIndelTest
Running test case halRearrangementInsertionTest
Running test case halRearrangementSimpleInversionTest
Running test case halRearrangementGappedInversionTest
Running test case halMappedSegmentMapExtraParalogsTest
Running test case halMappedSegmentMapUpTest
Running test case halMappedSegmentMapDownTest
Running test case halMappedSegmentParseTest
Running test case halMappedSegmentMapAcrossTest
Running test case halMappedSegmentMapDupeTest
Running test case halMappedSegmentColCompareTestCheck1
Running test case halMappedSegmentColCompareTestCheck2
Running test case halMappedSegmentColCompareTest1
Running test case halValidateSmallTest
Running test case halValidateMediumTest
Running test case halValidateManyGenomesTest
running
..................................................

OK (50 tests)

[diekhans]

I am at a loss; if could find 'tmp_alignment.hal' and make it available, we might be able to figure it ouit:

RuntimeError: Command ['halSetMetadata', 'tmp_alignment.hal', 'CACTUS_COMMIT', 'c087fe129d8c337c7eab961cebd49c80bcc20ef3'] signaled SIGABRT: stdout=None

[francicco]

I don't follow you... F

[diekhans]

sorry, spell correction gone bad.

Note the halSetMetadata command is working on a file tmp_alignment.hal, we would need a copy of that to try to reproduce the problem.

[francicco]

Ok, where do I suppose to find it? It doesn't appear anywhere. F

[diekhans]

It looks like it is in the local directory of the node:

src/cactus/progressive/cactus_progressive.py HALPath = "tmp_alignment.hal"

I have no idea where this would be, however you could modify the code to store it in some global location, provide a unique name is generated for it so it doesn't collide with others.

You could also put in a try/except and save the file if it fails

sorry, I can't be more specific.

[francicco]

you mean the --workDir location? F

[diekhans]

it could actually be in workDir, do a search. If not, it would be in some tmp location on the host.

[francicco]

Ok... I changed that line and I spotted the tmp location. I'm rerunning it. F

[francicco]

It looks like tmp_alignment.hal isn't generated. F

[diekhans]

from looking that the code and your log fie, I don't see how it couldn't be created. Maybe something is purging it

[francicco]

there's nothing. I also used --clean never F

[diekhans]

maybe try adding some to copy the tmp hal somewhere on failure???

[francicco]

How do I set the tmp location? F

[diekhans]

you would have to modify the code. Try adding something like this just before the code that fails

import sys
import tempfile
import shutil

tmpcp = tempfile.NamedTemporaryFile(suffix=".hal", prefix="tmp_alignment.", dir="/some/directory/", delete=False)

logger.warn("Saving HAL to %s" % tmpcp.filename)
print("Saving HAL to %s" % tmpcp.name, file=sys.stderr)
shutil.copyfile(HALPath, tmpcp.name)

[francicco]

I found two in the same node-0de51f24-9c4f-4a65-94d3-2400b38b86b8-932e55bc-e59d-4a2e-97a6-ca205a5a2da2 you want both? F

[francicco]

Here they are F

tmp_alignment.2.hal.gz tmp_alignment.1.hal.gz

[diekhans]

I did not get the error, can you try this on each of the HALs

halSetMetadata tmp_alignment.1.hal CACTUS_COMMIT c087fe129d8c337c7eab961cebd49c80bcc20ef3

and no need to compress HALs, there are already compressed

[francicco]

I know they are, but github didn't like .hal

I get this

HDF5-DIAG: Error detected in HDF5 (1.8.16) thread 0:
  #000: H5A.c line 249 in H5Acreate2(): no write intent on file
    major: Invalid arguments to routine
    minor: Write failed
terminate called after throwing an instance of 'H5::AttributeIException'
Aborted

F

[diekhans]

this seems to be a difference with the newer HDF5. halSetMetadata in the latest binary release doesn't exhibit the problem

https://github.com/ComparativeGenomicsToolkit/cactus/releases/download/v1.1.1/cactus-bin-v1.1.1.tar.gz

I will file a ticket on this issue with HAL

[diekhans]

Apparently, setting the environment variable HDF5_USE_FILE_LOCKING=FALSE will prevent this, but it would need to be propigated by Toul.

[francicco]

So, what should I do? F

[diekhans]

I would grab the binary release above; that doesn't show the problem.

Also, make sure your environment doesn't have any HDF5 variables set

env | grep HDF5

[francicco]

I was using that binary already:

[tk19812@bc4login1 cactus-bin-v1.1.1]$ env | grep HDF5
[tk19812@bc4login1 cactus-bin-v1.1.1]$ 
[tk19812@bc4login1 cactus-bin-v1.1.1]$ halSetMetadata tmp_alignment.2.hal CACTUS_COMMIT c087fe129d8c337c7eab961cebd49c80bcc20ef3
halSetMetadata: error while loading shared libraries: libsz.so.2: cannot open shared object file: No such file or directory

F