UnsatisfiedLinkError

[jshleap]

Hi, I am trying to run part of the benchmark to test the power9 nodes. I am having issues with GenomicsDBImport. Apparently is generating a library which AMD64 incompatible with Power PC platform. Any ideas?

$ /usr/bin/time -v -o time_GenomicsDBImport.log gatk --java-options -Xmx40g -Djava.library.path=/bio/apps/gatk_4.1.4/gatk-4.1.4.1/libs -DGATK_STACKTRACE_ON_USER_EXCEPTION=true -Djava.io.tmpdir=/tmp GenomicsDBImport -R /home/jshleap/projects/def-jshleap/IBM_benchmark/benchmark/Homo_sapiens_assembly38.fa --genomicsdb-workspace-path /home/jshleap/projects/def-jshleap/IBM_benchmark/benchmark/pon_db -V illuminaN.vcf.gz -L chr1 --tmp-dir=/home/jshleap/projects/def-jshleap/IBM_benchmark/benchmark

Using GATK jar /bio/apps/gatk_4.1.4/gatk-4.1.4.1/libs/gatk.jar defined in environment variable GATK_LOCAL
_JAR
Running:
    java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use
_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx40g -Djava.library.path=/bio/apps/gatk_4.1
.4/gatk-4.1.4.1/libs -DGATK_STACKTRACE_ON_USER_EXCEPTION=true -Djava.io.tmpdir=/tmp -jar /bio/apps/gatk_4
.1.4/gatk-4.1.4.1/libs/gatk.jar GenomicsDBImport -R /home/jshleap/projects/def-jshleap/IBM_benchmark/benc
hmark/Homo_sapiens_assembly38.fa --genomicsdb-workspace-path /home/jshleap/projects/def-jshleap/IBM_bench
mark/benchmark/pon_db -V illuminaN.vcf.gz -L chr1 --tmp-dir=/home/jshleap/projects/def-jshleap/IBM_benchm
ark/benchmark
14:58:45.950 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/bio/apps/gatk_4.1.4
/gatk-4.1.4.1/libs/gatk-package-4.1.4.1-local.jar!/com/intel/gkl/native/libgkl_compression.so
14:58:45.990 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compress
ion.so (/project/6047305/IBM_benchmark/benchmark/libgkl_compression7034410293743186653.so: /project/60473
05/IBM_benchmark/benchmark/libgkl_compression7034410293743186653.so: cannot open shared object file: No s
uch file or directory (Possible cause: can't load AMD 64-bit .so on a Power PC 64 LE-bit platform))
14:58:45.996 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/bio/apps/gatk_4.1.4
/gatk-4.1.4.1/libs/gatk-package-4.1.4.1-local.jar!/com/intel/gkl/native/libgkl_compression.so
14:58:46.014 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compress
ion.so (/project/6047305/IBM_benchmark/benchmark/libgkl_compression5293745742830896139.so: /project/60473
05/IBM_benchmark/benchmark/libgkl_compression5293745742830896139.so: cannot open shared object file: No s
uch file or directory (Possible cause: can't load AMD 64-bit .so on a Power PC 64 LE-bit platform))
Mar 13, 2020 2:58:46 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnCompute
Engine
INFO: Failed to detect whether we are running on Google Compute Engine.
14:58:46.397 INFO  GenomicsDBImport - ------------------------------------------------------------
14:58:46.398 INFO  GenomicsDBImport - The Genome Analysis Toolkit (GATK) v4.1.4.1-SNAPSHOT
14:58:46.398 INFO  GenomicsDBImport - For support and documentation go to https://software.broadinstitute.org/gatk/
14:58:46.398 INFO  GenomicsDBImport - Executing as jshleap@bio1 on Linux v4.18.0-80.7.2.el7.ppc64le ppc64le
14:58:46.398 INFO  GenomicsDBImport - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_242-b08
14:58:46.399 INFO  GenomicsDBImport - Start Date/Time: March 13, 2020 2:58:45 EDT PM
14:58:46.399 INFO  GenomicsDBImport - ------------------------------------------------------------
14:58:46.399 INFO  GenomicsDBImport - ------------------------------------------------------------
14:58:46.399 INFO  GenomicsDBImport - HTSJDK Version: 2.21.0
14:58:46.399 INFO  GenomicsDBImport - Picard Version: 2.21.2
14:58:46.399 INFO  GenomicsDBImport - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:58:46.399 INFO  GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:58:46.399 INFO  GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:58:46.399 INFO  GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:58:46.400 INFO  GenomicsDBImport - Deflater: JdkDeflater
14:58:46.400 INFO  GenomicsDBImport - Inflater: JdkInflater
14:58:46.400 INFO  GenomicsDBImport - GCS max retries/reopens: 20
14:58:46.400 INFO  GenomicsDBImport - Requester pays: disabled
14:58:46.400 INFO  GenomicsDBImport - Initializing engine
14:58:46.418 WARN  IntelDeflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
14:58:46.419 WARN  IntelDeflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
14:58:46.575 WARN  IntelDeflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
14:58:47.557 INFO  IntervalArgumentCollection - Processing 248956422 bp from intervals
14:58:47.894 INFO  GenomicsDBImport - Done initializing engine
14:58:48.464 INFO  GenomicsDBImport - Shutting down engine
[March 13, 2020 2:58:48 EDT PM] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.04 minutes.  
Runtime.totalMemory()=319291392
Exception in thread "main" java.lang.ExceptionInInitializerError
        at org.genomicsdb.GenomicsDBUtils.createTileDBWorkspace(GenomicsDBUtils.java:37)
        at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport.overwriteCreateOrCheckWorkspace(GenomicsDBImport.java:885)
        at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport.onTraversalStart(GenomicsDBImport.java:605)
        at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1046)
        at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:139)
        at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:191)
        at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:210)
        at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:163)
        at org.broadinstitute.hellbender.Main.mainEntry(Main.java:206)
        at org.broadinstitute.hellbender.Main.main(Main.java:292)
Caused by: org.genomicsdb.exception.GenomicsDBException: Could not load genomicsdb native library
        at org.genomicsdb.GenomicsDBUtilsJni.<clinit>(GenomicsDBUtilsJni.java:33)
        ... 10 more
Caused by: java.lang.UnsatisfiedLinkError: /project/6047305/IBM_benchmark/benchmark/libtiledbgenomicsdb6621924646570653205.so: /project/6047305/IBM_benchmark/benchmark/libtiledbgenomicsdb6621924646570653205.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64-bit .so on a Power PC 64 LE-bit platform)
        at java.lang.ClassLoader$NativeLibrary.load(Native Method)
        at java.lang.ClassLoader.loadLibrary0(ClassLoader.java:1946)
        at java.lang.ClassLoader.loadLibrary(ClassLoader.java:1828)
        at java.lang.Runtime.load0(Runtime.java:810)
        at java.lang.System.load(System.java:1088)
        at org.genomicsdb.GenomicsDBLibLoader.loadLibraryFromJar(GenomicsDBLibLoader.java:147)
        at org.genomicsdb.GenomicsDBLibLoader.loadLibrary(GenomicsDBLibLoader.java:47)
        at org.genomicsdb.GenomicsDBUtilsJni.<clinit>(GenomicsDBUtilsJni.java:30)
        ... 10 more