building Jellyfish with Intel compilers

[boegel]

Have you ever built Jellyfish with the Intel compilers?

The website mentions that GCC is required, and I've so far been unable to get it to build with icpc as a part of a Trinity (http://sourceforge.net/projects/trinityrnaseq) installation, I get stuck at:

$ make CXX=icpc V=1
...
/bin/sh ./libtool  --tag=CXX   --mode=compile icpc -DHAVE_CONFIG_H -I.  -Wnon-virtual-dtor -I.  -g -O3  -MT jellyfish/libjellyfish_la-read_parser.lo -MD -MP -MF jellyfish/.deps/libjellyfish_la-read_parser.Tpo -c -o jellyfish/libjellyfish_la-read_parser.lo `test -f 'jellyfish/read_parser.cc' || echo './'`jellyfish/read_parser.cc
libtool: compile:  icpc -DHAVE_CONFIG_H -I. -Wnon-virtual-dtor -I. -g -O3 -MT jellyfish/libjellyfish_la-read_parser.lo -MD -MP -MF jellyfish/.deps/libjellyfish_la-read_parser.Tpo -c jellyfish/read_parser.cc  -fPIC -DPIC -o jellyfish/.libs/libjellyfish_la-read_parser.o
./jellyfish/atomic_gcc.hpp(27): error: first argument must be a pointer to integer or enumeration type
        return __sync_val_compare_and_swap(ptr, oval, nval);
                                           ^
          detected during instantiation of "T atomic::gcc::add_fetch(volatile T *, T) [with T=unsigned long]" at line 54 of "./jellyfish/read_parser.hpp"

compilation aborted for jellyfish/read_parser.cc (code 2)
make[1]: *** [jellyfish/libjellyfish_la-read_parser.lo] Error 1

[jstjohn]

No I have not. Also I am not really an expert on this, you should really talk with the main developer, Guillaume Marcias, directly (http://www.cbcb.umd.edu/software/jellyfish/). I just patched jellyfish so I could use it to generate a uniqueness track.

On Dec 14, 2012, at 7:31 AM, Kenneth Hoste [email protected] wrote:

Have you ever built Jellyfish with the Intel compilers?

The website mentions that GCC is required, and I've so far been unable to get it to build with icpc as a part of a Trinity (http://sourceforge.net/projects/trinityrnaseq) installation, I get stuck at:

$ make CXX=icpc V=1
...
/bin/sh ./libtool --tag=CXX --mode=compile icpc -DHAVE_CONFIG_H -I. -Wnon-virtual-dtor -I. -g -O3 -MT jellyfish/libjellyfish_la-read_parser.lo -MD -MP -MF jellyfish/.deps/libjellyfish_la-read_parser.Tpo -c -o jellyfish/libjellyfish_la-read_parser.lo test -f 'jellyfish/read_parser.cc' || echo './'jellyfish/read_parser.cc
libtool: compile: icpc -DHAVE_CONFIG_H -I. -Wnon-virtual-dtor -I. -g -O3 -MT jellyfish/libjellyfish_la-read_parser.lo -MD -MP -MF jellyfish/.deps/libjellyfish_la-read_parser.Tpo -c jellyfish/read_parser.cc -fPIC -DPIC -o jellyfish/.libs/libjellyfish_la-read_parser.o
./jellyfish/atomic_gcc.hpp(27): error: first argument must be a pointer to integer or enumeration type
return __sync_val_compare_and_swap(ptr, oval, nval);
^
detected during instantiation of "T atomic::gcc::add_fetch(volatile T *, T) [with T=unsigned long]" at line 54 of "./jellyfish/read_parser.hpp"

compilation aborted for jellyfish/read_parser.cc (code 2)
make[1]: *** [jellyfish/libjellyfish_la-read_parser.lo] Error 1
—
Reply to this email directly or view it on GitHub.

[JensTimmerman]

JELLYFISH 1.1.10 works fine with intel compilers. So could this be included?

[jstjohn]

Fine with me. Go ahead and merge what I did into whatever you are working on.

On Apr 23, 2013, at 6:28 AM, Jens Timmerman [email protected] wrote:

JELLYFISH 1.1.10 works fine with intel compilers. So could this be included?

—
Reply to this email directly or view it on GitHub.