SciDB14.12 Install Error


#1

Hi, there!
I am Cherry. I encounter two questions when I install scidb14.12 according to the “SciDB_Build_Instructions_14.12.pdf”.

deployment/deploy.sh access root "" "" 192.168.1.37
deployment/deploy.sh access scidb "" "" 192.168.1.37

Q1: I have add the user scidb which can have access to run.py. There is no “sudo”. But it‘s wrong when I use “ ./run.py install”.

[scidb@yq scidbtrunk]$ sudo ./run.py install [sudo] password for scidb: WARNING: about to delete *all* contents of /home/scidb_source/scidbtrunk/stage/install/* [y]|n: [ 1%] Built target json_lib [ 1%] Built target MurmurHash_lib [ 8%] Built target util_lib [ 8%] Built target genmeta [ 8%] Built target catalog_lib [ 9%] Built target scidb_msg_lib [ 12%] Built target array_lib [ 15%] Built target system_lib [ 16%] Built target compression_lib [ 51%] Built target ops_lib [ 53%] Built target scalar_proc_lib [ 60%] Built target qproc_lib [ 61%] Built target io_lib [ 62%] Built target network_lib [ 62%] Built target scidb [ 67%] Built target scidbclient [ 68%] Built target scidbpython [ 68%] Built target dmalloc [ 68%] Built target mpi_common [ 69%] Built target mpi [ 70%] Built target scalapackForMPICH2 [ 72%] Built target mpi_slave_common [ 72%] Built target mpi_slave_direct [ 73%] Built target mpi_slave_scidb [ 78%] Built target dense_linear_algebra [ 78%] Built target linear_algebra [ 78%] Built target jdbc_build [ 78%] Built target benchGen [ 79%] Built target csv2scidb [ 79%] Built target osplitcsv [ 79%] Built target splitcsv [ 80%] Built target tsv2scidb [ 82%] Built target iquery [ 83%] Built target shim [ 83%] Built target shimsvc [ 83%] Built target dgenerator [ 83%] Built target gen_matrix [ 83%] Built target arg_separator [ 85%] Built target preparecdashreport [ 86%] Built target scidbtest [ 89%] Built target scidbtestharness [ 89%] Built target unit_tests [ 89%] Built target point [ 89%] Built target rational [ 90%] Built target complex [ 90%] Built target ra_decl [ 91%] Built target more_math [ 94%] Built target misc [ 95%] Built target match [ 96%] Built target bestmatch [ 97%] Built target savebmp [ 97%] Built target operators [ 99%] Built target fits [100%] Built target example_udos [100%] Built target tile_integration Install the project... -- Install configuration: "Debug" -- Installing: /home/scidb_source/scidbtrunk/stage/install/lib/libscidbclient.so -- Installing: /home/scidb_source/scidbtrunk/stage/install/bin/iquery -- Installing: /home/scidb_source/scidbtrunk/stage/install/bin/gen_matrix -- Installing: /home/scidb_source/scidbtrunk/stage/install/bin/benchGen -- Installing: /home/scidb_source/scidbtrunk/stage/install/bin/csv2scidb -- Installing: /home/scidb_source/scidbtrunk/stage/install/bin/tsv2scidb -- Installing: /home/scidb_source/scidbtrunk/stage/install/bin/scidbLoadCsv.sh -- Installing: /home/scidb_source/scidbtrunk/stage/install/bin/osplitcsv -- Installing: /home/scidb_source/scidbtrunk/stage/install/bin/splitcsv -- Installing: /home/scidb_source/scidbtrunk/stage/install/bin/loadcsv.py -- Installing: /home/scidb_source/scidbtrunk/stage/install/bin/loadpipe.py -- Installing: /home/scidb_source/scidbtrunk/stage/install/bin/calculate_chunk_length.py -- Installing: /home/scidb_source/scidbtrunk/stage/install/bin/remove_arrays.py -- Installing: /home/scidb_source/scidbtrunk/stage/install/bin/scidblib/PSF_license.txt -- Installing: /home/scidb_source/scidbtrunk/stage/install/bin/scidblib/__init__.py -- Installing: /home/scidb_source/scidbtrunk/stage/install/bin/scidblib/scidb_math.py -- Installing: /home/scidb_source/scidbtrunk/stage/install/bin/scidblib/scidb_progress.py -- Installing: /home/scidb_source/scidbtrunk/stage/install/bin/scidblib/scidb_schema.py -- Installing: /home/scidb_source/scidbtrunk/stage/install/bin/scidblib/scidb_afl.py -- Installing: /home/scidb_source/scidbtrunk/stage/install/bin/scidblib/statistics.py -- Installing: /home/scidb_source/scidbtrunk/stage/install/bin/scidblib/util.py -- Installing: /home/scidb_source/scidbtrunk/stage/install/bin/scidblib/counter.py -- Installing: /home/scidb_source/scidbtrunk/stage/install/bin/scidblib/scidb_psf.py -- Installing: /home/scidb_source/scidbtrunk/stage/install/jdbc/scidb4j.jar -- Installing: /home/scidb_source/scidbtrunk/stage/install/jdbc/jiquery.jar -- Installing: /home/scidb_source/scidbtrunk/stage/install/jdbc/example.jar -- Installing: /home/scidb_source/scidbtrunk/stage/install/jdbc/jdbctest.jar -- Installing: /home/scidb_source/scidbtrunk/stage/install/bin/unit_tests -- Installing: /home/scidb_source/scidbtrunk/stage/install/bin/scidbtestharness -- Installing: /home/scidb_source/scidbtrunk/stage/install/bin/shim -- Installing: /home/scidb_source/scidbtrunk/stage/install/bin/shimsvc -- Installing: /home/scidb_source/scidbtrunk/stage/install/bin/arg_separator -- Installing: /home/scidb_source/scidbtrunk/stage/install/bin/scidbtestprep.py -- Installing: /home/scidb_source/scidbtrunk/stage/install/bin/mu_admin.py -- Installing: /home/scidb_source/scidbtrunk/stage/install/etc/daemon.py -- Installing: /home/scidb_source/scidbtrunk/stage/install/etc/mu_config.ini -- Installing: /home/scidb_source/scidbtrunk/stage/install/etc/log4j.properties -- Installing: /home/scidb_source/scidbtrunk/stage/install/lib/libdmalloc.so -- Installing: /home/scidb_source/scidbtrunk/stage/install/lib/scidb/plugins/libpoint.so -- Installing: /home/scidb_source/scidbtrunk/stage/install/lib/scidb/plugins/libmatch.so -- Installing: /home/scidb_source/scidbtrunk/stage/install/lib/scidb/plugins/libbestmatch.so -- Installing: /home/scidb_source/scidbtrunk/stage/install/lib/scidb/plugins/librational.so -- Installing: /home/scidb_source/scidbtrunk/stage/install/lib/scidb/plugins/libcomplex.so -- Installing: /home/scidb_source/scidbtrunk/stage/install/lib/scidb/plugins/libra_decl.so -- Installing: /home/scidb_source/scidbtrunk/stage/install/lib/scidb/plugins/libmore_math.so -- Installing: /home/scidb_source/scidbtrunk/stage/install/lib/scidb/plugins/libmisc.so -- Installing: /home/scidb_source/scidbtrunk/stage/install/lib/scidb/plugins/libtile_integration.so -- Installing: /home/scidb_source/scidbtrunk/stage/install/lib/scidb/plugins/libfits.so -- Installing: /home/scidb_source/scidbtrunk/stage/install/lib/scidb/plugins/libmpi.so -- Installing: /home/scidb_source/scidbtrunk/stage/install/lib/scidb/plugins/libdense_linear_algebra-scidb.so -- Installing: /home/scidb_source/scidbtrunk/stage/install/lib/scidb/plugins/liblinear_algebra-scidb.so -- Installing: /home/scidb_source/scidbtrunk/stage/install/lib/scidb/plugins/libexample_udos.so -- Installing: /home/scidb_source/scidbtrunk/stage/install/lib/scidb/plugins/mpi_slave_scidb -- Installing: /home/scidb_source/scidbtrunk/stage/install/bin/bellman_ford_example.sh -- Installing: /home/scidb_source/scidbtrunk/stage/install/bin/pagerank_example.sh -- Installing: /home/scidb_source/scidbtrunk/stage/install/bin/scidb -- Installing: /home/scidb_source/scidbtrunk/stage/install/bin/scidb-prepare-db.sh -- Installing: /home/scidb_source/scidbtrunk/stage/install/bin/init-db.sh -- Installing: /home/scidb_source/scidbtrunk/stage/install/bin/scidb.py -- Installing: /home/scidb_source/scidbtrunk/stage/install/bin/scidb_backup.py -- Installing: /home/scidb_source/scidbtrunk/stage/install/bin/scidb_cores -- Installing: /home/scidb_source/scidbtrunk/stage/install/share/scidb/meta.sql -- Installing: /home/scidb_source/scidbtrunk/stage/install/share/scidb/log4cxx.properties -- Installing: /home/scidb_source/scidbtrunk/stage/install/etc/scidb-sample.conf -- Installing: /home/scidb_source/scidbtrunk/stage/install/etc/sample_config.ini -- Installing: /home/scidb_source/scidbtrunk/stage/install/lib/scidb/modules/prelude.txt -- Installing: /home/scidb_source/scidbtrunk/stage/install/lib/_libscidbpython.so -- Installing: /home/scidb_source/scidbtrunk/stage/install/lib/libscidbpython.py -- Installing: /home/scidb_source/scidbtrunk/stage/install/lib/scidbapi.py -- Installing: /home/scidb_source/scidbtrunk/stage/install/share/scidb/examples/python/README -- Installing: /home/scidb_source/scidbtrunk/stage/install/share/scidb/examples/python/sample.py -- Installing: /home/scidb_source/scidbtrunk/stage/install/share/scidb/examples/python/simplearray.data -- Installing: /home/scidb_source/scidbtrunk/stage/install/share/scidb/examples/python/sample2.py -- Installing: /home/scidb_source/scidbtrunk/stage/install/share/scidb/examples/python/sample2.csv -- Installing: /home/scidb_source/scidbtrunk/stage/install/share/scidb/examples/python/log4cxx.properties -- Installing: /home/scidb_source/scidbtrunk/stage/install/include -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/util -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/util/FileIO.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/util/Notification.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/util/ThreadPool.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/util/arena -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/util/arena/LimitedArena.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/util/arena/String.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/util/arena/Vector.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/util/arena/ArenaDecorator.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/util/arena/Managed.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/util/arena/ScopedArena.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/util/arena/ArenaMonitor.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/util/arena/Set.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/util/arena/Map.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/util/arena/List.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/util/arena/UnorderedMap.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/util/arena/Deque.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/util/arena/UnorderedSet.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/util/iqsort.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/util/shm -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/util/shm/SharedMemoryIpc.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/util/Thread.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/util/BitManip.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/util/WorkQueue.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/util/PluginObjects.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/util/ArrayCoordinatesMapper.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/util/StringUtil.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/util/CoordinatesToKey.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/util/Singleton.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/util/Atomic.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/util/Job.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/util/Platform.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/util/Lru.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/util/MultiConstIterators.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/util/PointerRange.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/util/Counter.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/util/ValueVector.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/util/TsvParser.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/util/JobQueue.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/util/SpatialType.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/util/Mutex.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/util/OverlappingChunksIterator.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/util/Barrier.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/util/Arena.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/util/SchemaUtils.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/util/NetworkMessage.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/util/Utility.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/util/InjectedError.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/util/Algorithm.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/util/RegionCoordinatesIterator.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/util/Network.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/util/MallocStats.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/util/RWLock.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/util/Hashing.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/util/CsvParser.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/util/Semaphore.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/util/Event.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/util/LockManager.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/util/Timing.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/util/CoordinatesMapper.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/util/forced_lexical_cast.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/util/DataStore.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/system -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/system/ShortErrors.inc -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/system/LongErrors.inc -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/system/ErrorsLibrary.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/system/Cluster.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/system/SystemCatalog.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/system/Config.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/system/Exceptions.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/system/Sysinfo.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/system/Constants.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/system/Warnings.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/system/ErrorCodes.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/system/Resources.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/system/Utils.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/system/BlockCyclic.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/query -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/query/Aggregate.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/query/AttributeComparator.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/query/QueryPlanUtilites.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/query/OperatorLibrary.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/query/SGChunkReceiver.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/query/TileFunctions.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/query/FunctionLibrary.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/query/FunctionDescription.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/query/Operator.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/query/Value.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/query/ParsingContext.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/query/Statistics.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/query/Expression.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/query/LogicalExpression.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/query/TypeSystem.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/query/Query.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/delta -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/mpi -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/mpi/MPISlaveProxy.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/mpi/MPILauncher.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/mpi/MPIUtils.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/mpi/MPIManager.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/mpi/MPIPhysical.hpp -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/dense_linear_algebra -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/dense_linear_algebra/blas -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/dense_linear_algebra/blas/initMathLibs.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/array -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/array/Coordinate.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/array/DBArray.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/array/MergeSortArray.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/array/Compressor.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/array/StreamArray.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/array/ParallelAccumulatorArray.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/array/MemChunk.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/array/RowCollection.cpp -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/array/Array.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/array/RowCollection.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/array/AllocationBuffer.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/array/BitmaskUnitTests.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/array/TransientCache.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/array/SortArray.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/array/ProjectArray.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/array/TileIteratorAdaptors.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/array/RLE.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/array/SpatialRangesChunkPosIterator.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/array/Tile.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/array/Metadata.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/array/MemArray.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/array/TupleArray.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/array/DelegateArray.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/array/TileInterface.h -- Installing: /home/scidb_source/scidbtrunk/stage/install/include/SciDBAPI.h is the result Adding user mydb... CREATE ROLE Creating language plpgsql for database ... UPDATE 1 GRANT Sample of connection string: host=localhost port=5432 dbname=mydb user=mydb password=mydb [b]/home/scidb_source/scidbtrunk/stage/install/bin/scidb.py: ERROR: ssh failure: server=127.0.0.1 port=22 Authentication failed.[/b] ./run.py: ERROR: Command install failed: Abnormal return code: 1 on command ['/home/scidb_source/scidbtrunk/stage/install/bin/scidb.py', 'initall-force', 'mydb', '/home/scidb_source/scidbtrunk/stage/install/etc/config.ini'] Make sure commands setup,make,install,start are performed (in that order) before stop,stopForce,tests [scidb@yq scidbtrunk]$ ssh 127.0.0.1 Warning: Permanently added '127.0.0.1' (RSA) to the list of known hosts. Last login: Sun Apr 19 10:51:18 2015 from scidb [scidb@yq ~]$ exit logout Connection to 127.0.0.1 closed.
Q2: “./run.py make -j4” is 100% and OK. And “ssh 127.0.0.1 ,ssh localhost, ssh 192.168.1.37” is OK. But why “/home/scidb_source/scidbtrunk/stage/install/bin/scidb.py: ERROR: ssh failure: server=127.0.0.1 port=22 Authentication failed.”?
Thanks a lot.


#2

Make sure that the directory where you have built scidb has read/write permissions for user scidb and its group.

Passwordless ssh access is created on a per-user basis: if you used sudo to set up passwordless access then it is possible that scidb user does not have passwordless access. Please do not use sudo for run.py operations: change user to scidb and repeat all of the steps (create passwordless access for scidb and root, etc.)