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
>
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