Hi Sébastien,
Given your results, we went with a clean install of CentOS5.9 and a new
download of Ray2.2, and the install went without a hitch.
The trouble shooting assistance is very much appreciated.
Cheers,
Anthony
On 28/08/2013, at 6:00 AM, Sébastien Boisvert wrote:
> On 26/08/13 09:48 PM, Anthony Borneman wrote:
>> Hi,
>>
>> I am having problems installing Ray v2.2.0 on our assembly rig under
>> CentOS5.9. Ray v2.1 installs and runs without any problems using the exact
>> same make instructions.
>>
>
> Hello,
>
> From the errors below, it seems that one header was not included
> ("constants.h" defines all these things I think).
>
> Anyway, I installed CentOS 5.9 to reproduce your rig setup, but I could not
> reproduce the problem:
>
>
> [seb@localhost Ray-v2.2.0]$ cat /etc/redhat-release
> CentOS release 5.9 (Final)
>
> [seb@localhost Ray-v2.2.0]$ sudo yum install -yyyyyyy openmpi openmpi-devel
> gcc-c++ zlib-devel bzip2-devel
>
>
> [seb@localhost Ray-v2.2.0]$ wget
> http://sourceforge.net/projects/denovoassembler/files/Ray-v2.2.0.tar.bz2
> [seb@localhost Ray-v2.2.0]$ tar -xjf Ray-v2.2.0.tar.bz2
> [seb@localhost Ray-v2.2.0]$ cd Ray-v2.2.0
> [seb@localhost Ray-v2.2.0]$ make HAVE_LIBZ=y HAVE_LIBBZ2=y MAXKMERLENGTH=64
> MPICXX=/usr/lib64/openmpi/1.4-gcc/bin/mpicxx
>
> [seb@localhost Ray-v2.2.0]$ file Ray
> Ray: ELF 64-bit LSB executable, AMD x86-64, version 1 (SYSV), for GNU/Linux
> 2.6.9, dynamically linked (uses shared libs), not stripped
>
>
> Versions of software on my CentOS 5.9 installation:
>
>
> [seb@localhost Ray-v2.2.0]$ yum list centos-release openmpi openmpi-devel
> gcc-c++ zlib-devel bzip2-devel
> Loaded plugins: downloadonly, fastestmirror, security
> Installed Packages
> bzip2-devel.i386
> 1.0.3-6.el5_5
> installed
> bzip2-devel.x86_64
> 1.0.3-6.el5_5
> installed
> centos-release.x86_64
> 10:5-9.el5.centos.1
> installed
> gcc-c++.x86_64
> 4.1.2-54.el5
> installed
> openmpi.i386
> 1.4-7.el5
> installed
> openmpi.x86_64
> 1.4-7.el5
> installed
> openmpi-devel.i386
> 1.4-7.el5
> installed
> openmpi-devel.x86_64
> 1.4-7.el5
> installed
> zlib-devel.i386
> 1.2.3-7.el5
> installed
> zlib-devel.x86_64
> 1.2.3-7.el5
> installed
>
>
>
>
> Did you modify the source code of Ray v2.2.0 ?
>
>
>
> -Sébastien
>
>
>> I have listed the output of the make command below.
>>
>> Any help would be appreciated.
>>
>> Cheers,
>>
>> Anthony
>>
>> $make HAVE_LIBZ=y HAVE_LIBBZ2=y MAXKMERLENGTH=64
>> MPICXX=/usr/lib64/openmpi/1.4-gcc/bin/mpicxx
>>
>> Compilation options (you can change them of course)
>>
>> PREFIX = install-prefix
>> MPICXX = /usr/lib64/openmpi/1.4-gcc/bin/mpicxx
>> MAXKMERLENGTH = 64
>> FORCE_PACKING = n
>> ASSERT = n
>> HAVE_LIBZ = y
>> HAVE_LIBBZ2 = y
>>
>> Compilation and linking flags (generated automatically)
>>
>> CXXFLAGS = -O3 -std=c++98 -Wall -g
>> CONFIG_FLAGS = -D CONFIG_MAXKMERLENGTH=64 -D CONFIG_HAVE_LIBZ -D
>> CONFIG_HAVE_LIBBZ2 -D CONFIG_RAY_VERSION="2.2.0"
>> LDFLAGS = -lz -lbz2
>>
>> make[1]: Entering directory `/scratch/aborneman/bin/Ray-v2.2.0/RayPlatform'
>> CXX RayPlatform/memory/ReusableMemoryStore.o
>> CXX RayPlatform/memory/MyAllocator.o
>> CXX RayPlatform/memory/RingAllocator.o
>> CXX RayPlatform/memory/allocator.o
>> CXX RayPlatform/memory/DefragmentationGroup.o
>> CXX RayPlatform/memory/ChunkAllocatorWithDefragmentation.o
>> CXX RayPlatform/memory/DefragmentationLane.o
>> CXX RayPlatform/routing/ConnectionGraph.o
>> CXX RayPlatform/routing/GraphImplementation.o
>> CXX RayPlatform/routing/GraphImplementationRandom.o
>> CXX RayPlatform/routing/GraphImplementationComplete.o
>> CXX RayPlatform/routing/GraphImplementationDeBruijn.o
>> CXX RayPlatform/routing/GraphImplementationKautz.o
>> CXX RayPlatform/routing/GraphImplementationExperimental.o
>> CXX RayPlatform/routing/GraphImplementationGroup.o
>> CXX RayPlatform/routing/Polytope.o
>> CXX RayPlatform/routing/Torus.o
>> CXX RayPlatform/communication/mpi_tags.o
>> CXX RayPlatform/communication/VirtualCommunicator.o
>> CXX RayPlatform/communication/BufferedData.o
>> CXX RayPlatform/communication/Message.o
>> CXX RayPlatform/communication/MessagesHandler.o
>> CXX RayPlatform/communication/MessageQueue.o
>> CXX RayPlatform/communication/MessageRouter.o
>> CXX RayPlatform/scheduling/VirtualProcessor.o
>> CXX RayPlatform/scheduling/TaskCreator.o
>> CXX RayPlatform/scheduling/SwitchMan.o
>> CXX RayPlatform/core/ComputeCore.o
>> CXX RayPlatform/core/MiniRank.o
>> core/MiniRank.h:36: warning: ‘class MiniRank’ has virtual functions but
>> non-virtual destructor
>> CXX RayPlatform/core/slave_modes.o
>> CXX RayPlatform/core/OperatingSystem.o
>> CXX RayPlatform/core/master_modes.o
>> CXX RayPlatform/core/statistics.o
>> CXX RayPlatform/plugins/CorePlugin.o
>> CXX RayPlatform/plugins/RegisteredPlugin.o
>> CXX RayPlatform/structures/StaticVector.o
>> CXX RayPlatform/profiling/Profiler.o
>> CXX RayPlatform/profiling/Derivative.o
>> CXX RayPlatform/profiling/TickLogger.o
>> CXX RayPlatform/profiling/TimePrinter.o
>> CXX RayPlatform/handlers/MasterModeExecutor.o
>> CXX RayPlatform/handlers/SlaveModeExecutor.o
>> CXX RayPlatform/handlers/MessageTagExecutor.o
>> CXX RayPlatform/cryptography/crypto.o
>> AR libRayPlatform.a
>> make[1]: Leaving directory `/scratch/aborneman/bin/Ray-v2.2.0/RayPlatform'
>> CXX code/Partitioner/Partitioner.o
>> ./code/SequencesIndexer/PairedRead.h:42: error: ‘LibraryHandle’ does not
>> name a type
>> ./code/SequencesIndexer/PairedRead.h:45: error: ‘Rank’ does not name a type
>> ./code/SequencesIndexer/PairedRead.h:47: error: ‘ReadHandle’ does not name a
>> type
>> ./code/SequencesLoader/Read.h:63: error: ‘Kmer’ does not name a type
>> ./code/SequencesLoader/Read.h:83: error: conflicting declaration ‘Read
>> ATTRIBUTE_PACKED’
>> ./code/SequencesIndexer/PairedRead.h:52: error: ‘ATTRIBUTE_PACKED’ has a
>> previous declaration as ‘PairedRead ATTRIBUTE_PACKED’
>> ./code/SequencesLoader/ArrayOfReads.h:38: error: ‘LargeCount’ does not name
>> a type
>> ./code/SequencesLoader/ArrayOfReads.h:39: error: ‘LargeCount’ does not name
>> a type
>> ./code/SequencesLoader/ArrayOfReads.h:49: error: expected ‘;’ before ‘(’
>> token
>> ./code/SequencesLoader/ArrayOfReads.h:50: error: declaration of ‘operator[]’
>> as non-function
>> ./code/SequencesLoader/ArrayOfReads.h:50: error: expected ‘;’ before ‘(’
>> token
>> ./code/SequencesLoader/ArrayOfReads.h:51: error: ‘LargeCount’ does not name
>> a type
>> ./code/SequencesLoader/LoaderInterface.h:36: warning: ‘class
>> LoaderInterface’ has virtual functions but non-virtual destructor
>> ./code/SequencesLoader/FastqLoader.h:41: warning: ‘class FastqLoader’ has
>> virtual functions but non-virtual destructor
>> ./code/SequencesLoader/FastaLoaderForReads.h:42: warning: ‘class
>> FastaLoaderForReads’ has virtual functions but non-virtual destructor
>> ./code/SequencesLoader/ExportLoader.h:46: warning: ‘class ExportLoader’ has
>> virtual functions but non-virtual destructor
>> ./code/SequencesLoader/ColorSpaceLoader.h:42: warning: ‘class
>> ColorSpaceLoader’ has virtual functions but non-virtual destructor
>> ./code/SequencesLoader/SffLoader.h:42: warning: ‘class SffLoader’ has
>> virtual functions but non-virtual destructor
>> ./code/SequencesLoader/FastqGzLoader.h:43: warning: ‘class FastqGzLoader’
>> has virtual functions but non-virtual destructor
>> ./code/SequencesLoader/FastaGzLoader.h:43: warning: ‘class FastaGzLoader’
>> has virtual functions but non-virtual destructor
>> ./code/SequencesLoader/FastqBz2Loader.h:41: warning: ‘class FastqBz2Loader’
>> has virtual functions but non-virtual destructor
>> ./code/SequencesLoader/FastaBz2Loader.h:41: warning: ‘class FastaBz2Loader’
>> has virtual functions but non-virtual destructor
>> ./code/SequencesLoader/Loader.h:49: error: ‘Rank’ does not name a type
>> ./code/SequencesLoader/Loader.h:56: error: ‘LargeIndex’ does not name a type
>> ./code/SequencesLoader/Loader.h:58: error: ‘LargeCount’ does not name a type
>> ./code/SequencesLoader/Loader.h:64: error: ‘Rank’ has not been declared
>> ./code/SequencesLoader/Loader.h:66: error: ‘LargeCount’ does not name a type
>> ./code/SequencesLoader/Loader.h:67: error: expected ‘;’ before ‘(’ token
>> code/Partitioner/Partitioner.h:88: error: ‘LargeCount’ was not declared in
>> this scope
>> code/Partitioner/Partitioner.h:88: error: template argument 2 is invalid
>> code/Partitioner/Partitioner.h:88: error: template argument 4 is invalid
>> code/Partitioner/Partitioner.h:90: error: ‘LargeCount’ was not declared in
>> this scope
>> code/Partitioner/Partitioner.h:90: error: template argument 2 is invalid
>> code/Partitioner/Partitioner.h:90: error: template argument 4 is invalid
>> code/Partitioner/Partitioner.h:100: error: ISO C++ forbids declaration of
>> ‘Parameters’ with no type
>> code/Partitioner/Partitioner.h:100: error: expected ‘;’ before ‘*’ token
>> code/Partitioner/Partitioner.h:105: error: ‘Parameters’ has not been declared
>> code/Partitioner/Partitioner.cpp:33: error: ‘Parameters’ has not been
>> declared
>> code/Partitioner/Partitioner.cpp: In member function ‘void
>> Partitioner::constructor(RingAllocator*, StaticVector*, StaticVector*, int*,
>> SwitchMan*)’:
>> code/Partitioner/Partitioner.cpp:40: error: ‘m_parameters’ was not declared
>> in this scope
>> code/Partitioner/Partitioner.cpp: In member function ‘void
>> Partitioner::call_RAY_MASTER_MODE_COUNT_FILE_ENTRIES()’:
>> code/Partitioner/Partitioner.cpp:53: error: ‘m_parameters’ was not declared
>> in this scope
>> code/Partitioner/Partitioner.cpp:61: error: ‘m_parameters’ was not declared
>> in this scope
>> code/Partitioner/Partitioner.cpp:71: error: ‘LargeCount’ was not declared in
>> this scope
>> code/Partitioner/Partitioner.cpp:71: error: expected `;' before ‘count’
>> code/Partitioner/Partitioner.cpp:72: error: invalid types ‘int[int]’ for
>> array subscript
>> code/Partitioner/Partitioner.cpp:74: error: ‘m_parameters’ was not declared
>> in this scope
>> code/Partitioner/Partitioner.cpp:77: error: ‘m_parameters’ was not declared
>> in this scope
>> code/Partitioner/Partitioner.cpp:83: error: ‘m_parameters’ was not declared
>> in this scope
>> code/Partitioner/Partitioner.cpp:85: error: request for member ‘size’ in
>> ‘((Partitioner*)this)->Partitioner::m_masterCounts’, which is of non-class
>> type ‘int’
>> code/Partitioner/Partitioner.cpp:87: error: invalid types ‘int[int]’ for
>> array subscript
>> code/Partitioner/Partitioner.cpp:88: error: invalid types ‘int[int]’ for
>> array subscript
>> code/Partitioner/Partitioner.cpp:90: error: request for member ‘clear’ in
>> ‘((Partitioner*)this)->Partitioner::m_masterCounts’, which is of non-class
>> type ‘int’
>> code/Partitioner/Partitioner.cpp:111: error: ‘LargeCount’ was not declared
>> in this scope
>> code/Partitioner/Partitioner.cpp:111: error: expected `;' before
>> ‘totalSequences’
>> code/Partitioner/Partitioner.cpp:116: error: expected `;' before ‘entries’
>> code/Partitioner/Partitioner.cpp:117: error: ‘entries’ was not declared in
>> this scope
>> code/Partitioner/Partitioner.cpp:120: error: ‘totalSequences’ was not
>> declared in this scope
>> code/Partitioner/Partitioner.cpp:128: error: ‘totalSequences’ was not
>> declared in this scope
>> code/Partitioner/Partitioner.cpp:133: error: ‘totalSequences’ was not
>> declared in this scope
>> code/Partitioner/Partitioner.cpp:140: error: ‘totalSequences’ was not
>> declared in this scope
>> code/Partitioner/Partitioner.cpp:153: error: expected `;' before ‘perRank’
>> code/Partitioner/Partitioner.cpp:156: error: ‘LargeIndex’ was not declared
>> in this scope
>> code/Partitioner/Partitioner.cpp:156: error: expected `;' before ‘first’
>> code/Partitioner/Partitioner.cpp:157: error: expected `;' before ‘last’
>> code/Partitioner/Partitioner.cpp:160: error: ‘last’ was not declared in this
>> scope
>> code/Partitioner/Partitioner.cpp:163: error: expected `;' before ‘count’
>> code/Partitioner/Partitioner.cpp:165: error: ‘first’ was not declared in
>> this scope
>> code/Partitioner/Partitioner.cpp:165: error: ‘last’ was not declared in this
>> scope
>> code/Partitioner/Partitioner.cpp: In member function ‘void
>> Partitioner::call_RAY_SLAVE_MODE_COUNT_FILE_ENTRIES()’:
>> code/Partitioner/Partitioner.cpp:184: error: ‘m_parameters’ was not declared
>> in this scope
>> code/Partitioner/Partitioner.cpp:191: error: ‘LargeCount’ was not declared
>> in this scope
>> code/Partitioner/Partitioner.cpp:191: error: expected `;' before ‘sequences’
>> code/Partitioner/Partitioner.cpp:193: error: ‘sequences’ was not declared in
>> this scope
>> code/Partitioner/Partitioner.cpp:200: error: invalid types ‘int[int]’ for
>> array subscript
>> code/Partitioner/Partitioner.cpp:211: error: ‘m_parameters’ was not declared
>> in this scope
>> code/Partitioner/Partitioner.cpp:221: error: request for member ‘size’ in
>> ‘((Partitioner*)this)->Partitioner::m_slaveCounts’, which is of non-class
>> type ‘int’
>> code/Partitioner/Partitioner.cpp:224: error: ‘LargeCount’ was not declared
>> in this scope
>> code/Partitioner/Partitioner.cpp:224: error: template argument 2 is invalid
>> code/Partitioner/Partitioner.cpp:224: error: template argument 4 is invalid
>> code/Partitioner/Partitioner.cpp:224: error: expected initializer before ‘i’
>> code/Partitioner/Partitioner.cpp:225: error: ‘i’ was not declared in this
>> scope
>> code/Partitioner/Partitioner.cpp:225: error: request for member ‘end’ in
>> ‘((Partitioner*)this)->Partitioner::m_slaveCounts’, which is of non-class
>> type ‘int’
>> code/Partitioner/Partitioner.cpp:227: error: expected `;' before ‘sequences’
>> code/Partitioner/Partitioner.cpp:229: error: ‘sequences’ was not declared in
>> this scope
>> code/Partitioner/Partitioner.cpp:245: error: invalid types ‘int[int]’ for
>> array subscript
>> code/Partitioner/Partitioner.cpp:245: error: ‘class Loader’ has no member
>> named ‘size’
>> code/Partitioner/Partitioner.cpp:249: error: invalid types ‘int[int]’ for
>> array subscript
>> code/Partitioner/Partitioner.cpp:268: error: invalid types ‘int[int]’ for
>> array subscript
>> code/Partitioner/Partitioner.cpp:281: error: request for member ‘clear’ in
>> ‘((Partitioner*)this)->Partitioner::m_slaveCounts’, which is of non-class
>> type ‘int’
>> make: *** [code/Partitioner/Partitioner.o] Error 1
>>
>>
>> Anthony Borneman
>> Principal Research Scientist - Molecular Biology | The Australian Wine
>> Research Institute
>> Waite Precinct, Hartley Grove cnr Paratoo Road, Urrbrae (Adelaide) SA 5064 |
>> Map
>> PO Box 197, Glen Osmond SA 5064, Australia
>> T: +61 8 83136613 (direct) | F: +61 8 83136601 |
>> www: www.awri.com.au | AWRI Events
>>
>> This communication, including attachments, is intended only for the
>> addressee(s) and contains information which might be confidential and/or the
>> copyright of The Australian Wine Research Institute (AWRI) or a third party.
>> If you are not the intended recipient of this communication please
>> immediately delete and destroy all copies and contact the sender. If you are
>> the intended recipient of this communication you should not copy, disclose
>> or distribute any of the information contained herein without the consent of
>> the AWRI and the sender. Any views expressed in this communication are those
>> of the individual sender except where the sender specifically states them to
>> be the views of the AWRI. No representation is made that this communication,
>> including attachments, is free of viruses. Virus scanning is recommended and
>> is the responsibility of the recipient.
>>
>>
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Anthony Borneman
Principal Research Scientist - Molecular Biology | The Australian Wine
Research Institute
Waite Precinct, Hartley Grove cnr Paratoo Road, Urrbrae (Adelaide) SA 5064 | Map
PO Box 197, Glen Osmond SA 5064, Australia
T: +61 8 83136613 (direct) | F: +61 8 83136601 |
www: www.awri.com.au | AWRI Events
This communication, including attachments, is intended only for the
addressee(s) and contains information which might be confidential and/or the
copyright of The Australian Wine Research Institute (AWRI) or a third party. If
you are not the intended recipient of this communication please immediately
delete and destroy all copies and contact the sender. If you are the intended
recipient of this communication you should not copy, disclose or distribute any
of the information contained herein without the consent of the AWRI and the
sender. Any views expressed in this communication are those of the individual
sender except where the sender specifically states them to be the views of the
AWRI. No representation is made that this communication, including attachments,
is free of viruses. Virus scanning is recommended and is the responsibility of
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