error: ‘PosixSpinLock’ in namespace ‘libmaus::parallel’ does not name a type

[tinyheero]

Hi,

I am trying to update my biobambam installation to the latest version and need to update my libmaus. When trying to install from source following a strategy I used to do, I am getting the following error:

libmaus/StaticInitialization.cpp:29: error: ‘PosixSpinLock’ in namespace ‘libmaus::parallel’ does not name a type
make[2]: *** [libmaus/libmaus_la-StaticInitialization.lo] Error 1
make[2]: Leaving directory `/clusterapp/clusterhome/fcchan/libmaus-0.0.127-release-20140602112423/src'

I ran the following commands for trying to build libmaus (0.0.127-release-20140602112423):

autoreconf -i -f
CPPFLAGS=-I$/home/${USER}/usr/local/include LDFLAGS=-L/home/${USER}/usr/local/lib ./configure --prefix=/home/${USER}/usr/local --with-io_lib=/home/${USER}/usr/local --with-snappy=/home/${USER}/usr/local --disable-shared-libmaus -disable-asm --disable-ssse3 --disable-sse4
make

I am using Centos 5.5 and have no control over this as I am working on a shared server.

Any help would be much appreciated. Thanks:

[gt1]

Hi,

I will look into it, but it may take a few days to find the time and set up a CentOS system in a virtual machine.

Best,

[gt1]

Hi,

I have looked into building libmaus/biobambam on CentOS 5.5 now. I have modified the code in the libmaus experimental branch to compile with glibc versions < 2.6, as not working with these versions would be a bug in libmaus. This solves part of the problem. The other problem is that the system compiler on CentOS 5.5 (gcc 4.1.2 with Redhat patches) cannot compile some of the tests in libmaus (this is particularly the tests in src/test/testutf8split.cpp). There is little I can or would want to do about this, because this is a bug in this particular version of gcc, not libmaus. Now you can do one of two things to get it compiled:

1. comment out the calling of the test in src/test/testutf8split.cpp and compile the rest
2. use a more recent compiler, the following script shows how to get one
   ftp://ngs.sanger.ac.uk/scratch/project/gt1/biobambam/biobambam_centos_5_5_build.sh . Please note that this will quite some time. This will compile gcc version 4.9. Using an older version could be faster (for compiling the compiler, not for running the resulting programs).

I hope this helps,

[gt1]

btw.: I wasn't able to reproduce the error concerning the spin locks on a fresh install of CentOS 5.5 using gcc 4.9 . Maybe I could see a bit more in a complete build log.

[tinyheero]

Thanks I'll give this a go.

[tinyheero]

Apologies of taking so long to get back to you. I have now just finally had a chance to look into this:

Given that the latest version now seems to be 0.0.167, I've taken the experimental branch of libmaus-0.0.167 and did the following:

autoreconf -i -f CPPFLAGS=-I$/home/${USER}/usr/local/include LDFLAGS=-L/home/${USER}/usr/local/lib ./configure --prefix=/home/${USER}/usr/local --with-io_lib=/home/${USER}/usr/local --with-snappy=/home/${USER}/usr/local --disable-shared-libmaus -disable-asm --disable-ssse3 --disable-sse4 make

How I still got the same error as before:

/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Ihome/fcchan/usr/local/include -I/home/fcchan/usr/local/include -W -Wall -Wabi -Wnon-virtual-dtor -Ihome/fcchan/usr/local/include -Ihome/fcchan/usr/local/include -O3 -rdynamic -pthread -fopenmp -MT libmaus/libmaus_la-StaticInitialization.lo -MD -MP -MF libmaus/.deps/libmaus_la-StaticInitialization.Tpo -c -o libmaus/libmaus_la-StaticInitialization.lotest -f 'libmaus/StaticInitialization.cpp' || echo './'libmaus/StaticInitialization.cppitialization.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Ihome/fcchan/usr/local/include -I/home/fcchan/usr/local/include -W -Wall -Wabi -Wnon-virtual-dtor -Ihome/fcchan/usr/local/include -Ihome/fcchan/usr/local/include -O3 -rdynamic -pthread -fopenmp -MT libmaus/libmaus_la-StaticInitialization.lo -MD -MP -MF libmaus/.deps/libmaus_la-StaticInitialization.Tpo -c libmaus/StaticInitialization.cpp -fPIC -DPIC -o libmaus/.libs/libmaus_la-StaticInitialization.oInitialization.o libmaus/StaticInitialization.cpp:29: error: ‘PosixSpinLock’ in namespace ‘libmaus::parallel’ does not name a type make[2]: *** [libmaus/libmaus_la-StaticInitialization.lo] Error 1 make[2]: Leaving directory/clusterapp/clusterhome/fcchan/libmaus-libmaus_experimental_0_0_167/src'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory /clusterapp/clusterhome/fcchan/libmaus-libmaus_experimental_0_0_167' make: *** [all] Error 2

The ./configure log can be found here:

https://gist.github.com/tinyheero/8a945fbfcc74443f2c28

The make log can be found here:

https://gist.github.com/tinyheero/97244733f05b823068dd

[gt1]

Could you please add the contents of src/libmaus/LibMausConfig.hpp ?

[tinyheero]

Add it here:

https://gist.github.com/tinyheero/b6ca6f2ab8bd07290c9f

[tinyheero]

Hi,

Was just wondering if there has been any luck with diagnosing the issue?

Thanks,

[gt1]

Hi,

I have reformulated some of the code. But as I cannot reproduce the issue myself, it is a bit tricky.

[tinyheero]

Yes not sure why it appears only on the system that I am building it on. Is there a "re-patched" version I can try to see if any of the reformulation have worked?

[gt1]

You could try the latest experimental version. I have replaced the checks for posix threads in some of the relevant files by checks for posix spin locks.

[tinyheero]

Downloaded the libmaus_0_0_170 version and did the same configure, make. I ran into a snappy issue and re-installed the latest version (1.2.0). This resolved that issue, but then:

But then during the make of libmaus I get this error:
...
/bin/sh ../libtool --tag=CXX --mode=link g++ -O3 -rdynamic -pthread -fopenmp -L/home/fong/usr/local/lib -o testpacdecode test/testpacdecode.o libmaus.la -lrt -L/home/fong/usr/local/lib -lz
libtool: link: g++ -O3 -rdynamic -pthread -fopenmp -o testpacdecode test/testpacdecode.o -L/home/fong/usr/local/lib ./.libs/libmaus.a -ldl /home/fong/usr/local/lib/libsnappy.a -lrt -lz -fopenmp -pthread
Makefile:4440: warning: undefined variable V' Makefile:4440: warning: undefined variableINCLUDES'
Makefile:4440: warning: undefined variable AM_CPPFLAGS' Makefile:4440: warning: undefined variable/'
Makefile:4440: warning: undefined variable /' Makefile:4440: warning: undefined variableAM_CXXFLAGS'
depbase=echo test/testutf8split.o | sed 's|[^/]*$|.deps/&|;s|\.o$||';
g++ -DHAVE_CONFIG_H -I. -I.. -Ihome/fong/usr/local/include -Ihome/fong/usr/local/include -O3 -rdynamic -pthread -fopenmp -MT test/testutf8split.o -MD -MP -MF $depbase.Tpo -c -o test/testutf8split.o test/testutf8split.cpp &&
mv -f $depbase.Tpo $depbase.Po
test/testutf8split.cpp: In function ‘void testUtf8Seek(const std::string&)’:
test/testutf8split.cpp:150: warning: converting to ‘int64_t’ from ‘double’
./libmaus/wavelet/Utf8ToImpCompactHuffmanWaveletTree.hpp: In static member function ‘static void libmaus::wavelet::Utf8ToImpCompactHuffmanWaveletTree::constructWaveletTree(const std::string&, const std::string&, const libmaus::huffman::HuffmanTree*, uint64_t) [with bool radixsort = true]’:
./libmaus/wavelet/Utf8ToImpCompactHuffmanWaveletTree.hpp:71: internal compiler error: in find_outermost_region_in_block, at tree-cfg.c:4739
Please submit a full bug report,
with preprocessed source if appropriate.
See URL:http://bugzilla.redhat.com/bugzilla for instructions.
Preprocessed source stored into /tmp/cceZqC5b.out file, please attach this to your bugreport.

[gt1]

As the build process managed to reach this stage of the compilation, the issue of this ticket (undefined class) seems resolved. The error reported in the compile log is a bug in the compiler, not in libmaus. I don't have issues compiling libmaus for older versions of Linux using gcc 4.1.2, but this particular version of gcc in use above seems broken. I have recently started to provide binaries for biobambam containing libmaus compiled for (not on) older Linux versions. I am obviously also happy to distribute the scripts I use for producing these. But I cannot fix the error above, because it is not an error in my code.

[gt1]

There is a new configure option --disable-compile-testprograms in versions >= 0.0.185. This will probably get you around the problem above.

[yangxiaofeill]

When I run make command, the error message like:
In file included from ./libmaus/parallel/SynchronousQueue.hpp:28:0, from ./libmaus/network/Socket.hpp:55, from ./libmaus/network/HttpHeader.hpp:23, from ./libmaus/network/HttpHeaderWrapper.hpp:22, from ./libmaus/network/HttpSocketInputStreamBuffer.hpp:22, from ./libmaus/network/UrlInputStreamBufferWrapper.hpp:22, from ./libmaus/network/UrlInputStream.hpp:22, from ./libmaus/network/UrlInputStreamFactory.hpp:23, from ./libmaus/aio/InputStreamFactoryContainer.hpp:24, from libmaus/StaticInitialization.cpp:206: ./libmaus/parallel/PosixSemaphore.hpp:52:4: error: 'sem_t' does not name a type sem_t * psemaphore; ^ ./libmaus/parallel/PosixSemaphore.hpp: In constructor 'libmaus::parallel::NamedPosixSemaphore::NamedPoonst string&, bool)': ./libmaus/parallel/PosixSemaphore.hpp:64:44: error: class 'libmaus::parallel::NamedPosixSemaphore' doe field named 'psemaphore' : semname(rsemname), primary(rprimary), psemaphore(0) ^ ./libmaus/parallel/PosixSemaphore.hpp:67:6: error: 'psemaphore' was not declared in this scope psemaphore = sem_open(semname.c_str(), O_CREAT | O_EXCL, 0700, 0); ^ ./libmaus/parallel/PosixSemaphore.hpp:67:70: error: 'sem_open' was not declared in this scope psemaphore = sem_open(semname.c_str(), O_CREAT | O_EXCL, 0700, 0); ^ ./libmaus/parallel/PosixSemaphore.hpp:69:6: error: 'psemaphore' was not declared in this scope psemaphore = sem_open(semname.c_str(), 0); ^ ./libmaus/parallel/PosixSemaphore.hpp:69:46: error: 'sem_open' was not declared in this scope psemaphore = sem_open(semname.c_str(), 0); ^ ./libmaus/parallel/PosixSemaphore.hpp:71:10: error: 'psemaphore' was not declared in this scope if ( psemaphore == SEM_FAILED ) ^ ./libmaus/parallel/PosixSemaphore.hpp:71:24: error: 'SEM_FAILED' was not declared in this scope if ( psemaphore == SEM_FAILED ) ^ In file included from ./libmaus/parallel/SynchronousQueue.hpp:28:0, from ./libmaus/network/Socket.hpp:55, from ./libmaus/network/HttpHeader.hpp:23, from ./libmaus/network/HttpHeaderWrapper.hpp:22, from ./libmaus/network/HttpSocketInputStreamBuffer.hpp:22, from ./libmaus/network/UrlInputStreamBufferWrapper.hpp:22, from ./libmaus/network/UrlInputStream.hpp:22, from ./libmaus/network/UrlInputStreamFactory.hpp:23, from ./libmaus/aio/InputStreamFactoryContainer.hpp:24, from libmaus/StaticInitialization.cpp:206: ./libmaus/parallel/PosixSemaphore.hpp: In destructor 'libmaus::parallel::NamedPosixSemaphore::~NamedPo': ./libmaus/parallel/PosixSemaphore.hpp:81:15: error: 'psemaphore' was not declared in this scope sem_close(psemaphore); ^ ./libmaus/parallel/PosixSemaphore.hpp:81:25: error: 'sem_close' was not declared in this scope sem_close(psemaphore); ^ ./libmaus/parallel/PosixSemaphore.hpp:83:32: error: 'sem_unlink' was not declared in this scope sem_unlink(semname.c_str()); ^ ./libmaus/parallel/PosixSemaphore.hpp: In member function 'void libmaus::parallel::NamedPosixSemaphore ./libmaus/parallel/PosixSemaphore.hpp:88:45: error: 'psemaphore' was not declared in this scope while ( sem_post ( psemaphore ) != 0 ) ^ ./libmaus/parallel/PosixSemaphore.hpp:88:56: error: 'sem_post' was not declared in this scope while ( sem_post ( psemaphore ) != 0 ) ^ ./libmaus/parallel/PosixSemaphore.hpp: In member function 'void libmaus::parallel::NamedPosixSemaphore ./libmaus/parallel/PosixSemaphore.hpp:109:45: error: 'psemaphore' was not declared in this scope while ( sem_wait ( psemaphore ) != 0 ) ^ ./libmaus/parallel/PosixSemaphore.hpp:109:56: error: 'sem_wait' was not declared in this scope while ( sem_wait ( psemaphore ) != 0 ) ^ ./libmaus/parallel/PosixSemaphore.hpp: In member function 'bool libmaus::parallel::NamedPosixSemaphore ./libmaus/parallel/PosixSemaphore.hpp:131:48: error: 'psemaphore' was not declared in this scope while ( sem_trywait ( psemaphore ) != 0 ) ^ ./libmaus/parallel/PosixSemaphore.hpp:131:59: error: 'sem_trywait' was not declared in this scope while ( sem_trywait ( psemaphore ) != 0 ) ^ ./libmaus/parallel/PosixSemaphore.hpp: In member function 'int libmaus::parallel::NamedPosixSemaphore: ./libmaus/parallel/PosixSemaphore.hpp:159:47: error: 'psemaphore' was not declared in this scope int r = sem_getvalue(psemaphore,&v); ^ ./libmaus/parallel/PosixSemaphore.hpp:159:60: error: 'sem_getvalue' was not declared in this scope int r = sem_getvalue(psemaphore,&v); ^ ./libmaus/parallel/PosixSemaphore.hpp: At global scope: ./libmaus/parallel/PosixSemaphore.hpp:188:11: error: 'sem_t' does not name a type sem_t semaphore; ^ ./libmaus/parallel/PosixSemaphore.hpp:189:4: error: 'sem_t' does not name a type sem_t * psemaphore; ^ ./libmaus/parallel/PosixSemaphore.hpp: In constructor 'libmaus::parallel::PosixSemaphore::PosixSemapho ./libmaus/parallel/PosixSemaphore.hpp:196:44: error: class 'libmaus::parallel::PosixSemaphore' does nold named 'semaphore' PosixSemaphore() : semaphore(), psemaphore(0) ^ ./libmaus/parallel/PosixSemaphore.hpp:196:57: error: class 'libmaus::parallel::PosixSemaphore' does nold named 'psemaphore' PosixSemaphore() : semaphore(), psemaphore(0) ^ ./libmaus/parallel/PosixSemaphore.hpp:204:16: error: 'semaphore' was not declared in this scope memset ( & semaphore, 0, sizeof(sem_t) ); ^ ./libmaus/parallel/PosixSemaphore.hpp:204:37: error: 'sem_t' was not declared in this scope memset ( & semaphore, 0, sizeof(sem_t) ); ^ ./libmaus/parallel/PosixSemaphore.hpp:216:39: error: 'sem_init' was not declared in this scope if ( sem_init ( & semaphore, 0, 0 ) ) ^ ./libmaus/parallel/PosixSemaphore.hpp:223:5: error: 'psemaphore' was not declared in this scope psemaphore = &semaphore; ^ ./libmaus/parallel/PosixSemaphore.hpp: In destructor 'libmaus::parallel::PosixSemaphore::~PosixSemapho ./libmaus/parallel/PosixSemaphore.hpp:232:17: error: 'psemaphore' was not declared in this scope sem_destroy(psemaphore); ^ ./libmaus/parallel/PosixSemaphore.hpp:232:27: error: 'sem_destroy' was not declared in this scope sem_destroy(psemaphore); ^ ./libmaus/parallel/PosixSemaphore.hpp: In member function 'void libmaus::parallel::PosixSemaphore::pos ./libmaus/parallel/PosixSemaphore.hpp:238:45: error: 'psemaphore' was not declared in this scope while ( sem_post ( psemaphore ) != 0 ) ^ ./libmaus/parallel/PosixSemaphore.hpp:238:56: error: 'sem_post' was not declared in this scope while ( sem_post ( psemaphore ) != 0 ) ^ ./libmaus/parallel/PosixSemaphore.hpp: In member function 'void libmaus::parallel::PosixSemaphore::wai ./libmaus/parallel/PosixSemaphore.hpp:259:45: error: 'psemaphore' was not declared in this scope while ( sem_wait ( psemaphore ) != 0 ) ^ ./libmaus/parallel/PosixSemaphore.hpp:259:56: error: 'sem_wait' was not declared in this scope while ( sem_wait ( psemaphore ) != 0 ) ^ ./libmaus/parallel/PosixSemaphore.hpp: In member function 'bool libmaus::parallel::PosixSemaphore::try ./libmaus/parallel/PosixSemaphore.hpp:281:48: error: 'psemaphore' was not declared in this scope while ( sem_trywait ( psemaphore ) != 0 ) ^ ./libmaus/parallel/PosixSemaphore.hpp:281:59: error: 'sem_trywait' was not declared in this scope while ( sem_trywait ( psemaphore ) != 0 ) ^ ./libmaus/parallel/PosixSemaphore.hpp: In member function 'bool libmaus::parallel::PosixSemaphore::tim ./libmaus/parallel/PosixSemaphore.hpp:320:61: error: 'psemaphore' was not declared in this scope int const v = sem_timedwait(psemaphore,&waittime); ^ ./libmaus/parallel/PosixSemaphore.hpp:320:81: error: 'sem_timedwait' was not declared in this scope int const v = sem_timedwait(psemaphore,&waittime); ^ make[1]: *** [libmaus/libmaus_la-StaticInitialization.lo] Error 1 make[1]: Leaving directory /opt/software/libmaus/src'
make: *** [check-recursive] Error 1`

I don't know why and how to fix this prombel?