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**GenoMax** · 11-06-2013, 03:50 PM

Are you able to use the binary? That could solve this problem. http://cufflinks.cbcb.umd.edu/downlo..._x86_64.tar.gz

If not what cluster OS are you trying to compile on? Have you tried to use the newest boost lib?

**jor12345** · 11-06-2013, 11:46 PM

Can't use the binary

Code:

$ cufflinks ./test_data.sam
-bash: /scratch/martinsj/RNAseq/bin/cufflinks: cannot execute binary file

I've tried boost 1.54, 1.55 beta, and 1.47, error was always the same.

>>Cluster<<

Operating system: Linux
Number of nodes: 841
Number of cores: 9712
Memory: 35,5 TB

The node interconnect is based on InfiniBand QDR. INCA compute nodes providing two Intel Nehalem EP quad-core processors (Xeon X5550) and Intel Westmere hexa-core processors (Xeon X5650), respectively. MESCA nodes equipped with four Intel Nehalem EX octo-core processors (Xeon X7560).

Thanks!!

**dpryan** · 11-07-2013, 02:09 AM

This is probably due to the use of an ancient version of gcc (4.1.2 is 6.5 years old!).

The compilation is aborting due to

Code:

Fehler: Ganzzahlkonstante ist zu gross für >>long<<-Typ

or 'Error, integer constant is too large for type "long"' for us Ausländer. The cause of this is pretty apparent if you look at bundles.cpp:

Code:

if (tmp.ref_id() == 12638153115695167477)  // corresponds to SAM "*" under FNV hash. unaligned read record

You might be able to make the following change and get things to work:

Code:

if (tmp.ref_id() == 12638153115695167477ULL)  // corresponds to SAM "*" under FNV hash. unaligned read record

but I don't actually know if that version of g++ can handle that (a bit of googling suggests that this wasn't even in the C++ standard when that version of g++ was released!). If making that change works, then great. Otherwise, you'll probably just need to use a more recent version of gcc.

**GenoMax** · 11-07-2013, 04:09 AM

I will confirm Devon's assessment. You should try to upgrade the GCC (to the newest version if possible) otherwise even if you are able to get it to compile it will cause seg faults once you start running.

**jor12345** · 11-08-2013, 12:02 PM

Compiled and cufflinks test passed!

After getting updated gcc onto a private folder of the cluster I installed boost

Code:

cd boost_1_55_0b1
echo "using gcc : 4.8.2 : $scr/bin/g++ ; " >> tools/build/v2/user-config.jam
./bootstrap.sh --prefix=$scr --with-toolset=gcc
./bjam --prefix=$scr link=static \
 runtime-link=static stage install

and cufflinks using the new gcc and adding rt to the LIBS to correct another error relate to "time":

Code:

cd cufflinks-2.1.1
CC=$scr/bin/gcc CXX=$scr/bin/g++ ./configure --prefix=$scr --with-boost=$scr --with-boost-libdir=$scr/lib --with-eigen=$scr/include --with-bam=$scr
echo "LIBS = -lz -lrt" >> $scr/installation_files/cufflinks-2.1.1/src/Makefile
make
make install

Additionally I always have to export the LD_LIBRADY_PATH for the new lib before running cufflinks or tophat with the updated gcc.

Code:

export LD_LIBRARY_PATH=$scr/lib:$LD_LIBRARY_PATH

both tophat and cufflinks were able to analyse their respective testdata.

Thanks a lot guys!!

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HPC cluster : make error : make[2]: *** [bundles.o] Error 1

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