Entering edit mode
7.8 years ago
yvan.wenger
▴
20
Hello,
I would like to try kmergenie, but I can't compile (actually on my machine, Ubuntu 14.04.4 LTS, there is no problem, but on the server I would like to install it I get this error:
g++ -o minia/Pool.o -c minia/Pool.cpp -I/opt/rh/devtoolset-2/root/usr/include -pthread -D_largeint -DKMER_PRECISION=4
g++ -o minia/Bank.o -c minia/Bank.cpp -I/opt/rh/devtoolset-2/root/usr/include -pthread -D_largeint -DKMER_PRECISION=4
g++ -o minia/Hash16.o -c minia/Hash16.cpp -I/opt/rh/devtoolset-2/root/usr/include -pthread -D_largeint -DKMER_PRECISION=4
g++ -o minia/Bloom.o -c minia/Bloom.cpp -I/opt/rh/devtoolset-2/root/usr/include -pthread -D_largeint -DKMER_PRECISION=4
g++ -o minia/Kmer.o -c minia/Kmer.cpp -I/opt/rh/devtoolset-2/root/usr/include -pthread -D_largeint -DKMER_PRECISION=4
g++ -o minia/Utils.o -c minia/Utils.cpp -I/opt/rh/devtoolset-2/root/usr/include -pthread -D_largeint -DKMER_PRECISION=4
g++ -o minia/LinearCounter.o -c minia/LinearCounter.cpp -I/opt/rh/devtoolset-2/root/usr/include -pthread -D_largeint -DKMER_PRECISION=4
g++ -o minia/LargeInt.o -c minia/LargeInt.cpp -I/opt/rh/devtoolset-2/root/usr/include -pthread -D_largeint -DKMER_PRECISION=4
g++ -o minia/MultiConsumer.o -c minia/MultiConsumer.cpp -I/opt/rh/devtoolset-2/root/usr/include -pthread -D_largeint -DKMER_PRECISION=4
g++ -o minia/Hashing.o -c minia/Hashing.cpp -I/opt/rh/devtoolset-2/root/usr/include -pthread -D_largeint -DKMER_PRECISION=4
g++ -o specialk minia/Pool.o minia/Bank.o minia/Hash16.o minia/Bloom.o minia/Kmer.o minia/Utils.o minia/LinearCounter.o minia/LargeInt.o minia/MultiConsumer.o minia/Hashing.o main.cpp -I/opt/rh/devtoolset-2/root/usr/include -pthread -D_largeint -DKMER_PRECISION=4 -L/opt/rh/devtoolset-2/root/usr/lib64 -L/opt/rh/devtoolset-2/root/usr/lib -lz -DSVN_REV=1.7016
minia/Bank.o:Bank.cpp:function Bank::open_stream(int): error: undefined reference to 'gzopen64'
minia/Bank.o:Bank.cpp:function Bank::init(char**, int): error: undefined reference to 'gzopen64'
minia/Bank.o:Bank.cpp:function Bank::estimate_kmers_volume(int): error: undefined reference to 'gztell64'
minia/Bank.o:Bank.cpp:function Bank::estimate_kmers_volume(int): error: undefined reference to 'gztell64'
minia/Bank.o:Bank.cpp:function Bank::estimate_nb_reads(): error: undefined reference to 'gztell64'
minia/Bank.o:Bank.cpp:function Bank::estimate_nb_reads(): error: undefined reference to 'gztell64'
minia/Bank.o:Bank.cpp:function Bank::load_position(): error: undefined reference to 'gzseek64'
collect2: error: ld returned 1 exit status
make: *** [specialk] Error 1
Theoretically dependencies are met...
Currently Loaded Modules:
1) GCC/4.9.3-2.25 7) ScaLAPACK/2.0.2-OpenBLAS-0.2.15-LAPACK-3.6.0 13) Java/1.8.0_72 19) HDF5/1.8.16 25) bzip2/1.0.6 31) GCCcore/4.9.3 37) impi/5.1.2.150
2) numactl/2.0.11 8) ncurses/6.0 14) Tcl/8.6.4 20) netCDF/4.3.3.1 26) gettext/0.19.6 32) ifort/2016.1.150-GCC-4.9.3-2.25 38) python/33
3) hwloc/1.11.2 9) libreadline/6.3 15) Tk/8.6.4-no-X11 21) expat/2.1.0 27) XZ/5.2.2 33) iimpi/8.1.5-GCC-4.9.3-2.25
4) OpenMPI/1.10.2 10) libpng/1.6.21 16) cURL/7.47.0 22) GDAL/2.0.2 28) PCRE/8.38 34) binutils/2.25
5) OpenBLAS/0.2.15-LAPACK-3.6.0 11) NASM/2.11.08 17) libxml2/2.9.3 23) PROJ/4.9.2 29) R/3.3.1 35) zlib/1.2.8
6) FFTW/3.3.4 12) libjpeg-turbo/1.4.2 18) Szip/2.1 24) GMP/6.1.0 30) gcc/devtoolset 36) icc/2016.1.150-GCC-4.9.3-2.25
Do you have the
zlib-devel
package installed?This thread may be also of interest, if you do.
Sorry, I didn't reply the right way...
What do you get with
echo $LD_LIBRARY_PATH
?I think these two locations don't seem to have the zlib files (
-L/opt/rh/devtoolset-2/root/usr/lib64 -L/opt/rh/devtoolset-2/root/usr/lib
). Can you edit the Makefile for minia and add the location for your zlib files with another-L /opt/ebsofts/Compiler/GCCcore/4.9.3/zlib/1.2.8/lib
)? Or you could append this directory to yourLD_LIBRARY_PATH
as an alternative.Great, here is what I get:
I do not see a makefile in the minia directory, and if I need to add the location for the zlib file to the main makefile, how shoud I do it? I am not really an expert...
Can you try
What files are in
/opt/ebsofts/Compiler/GCCcore/4.9.3/zlib/1.2.8/lib
?The files in /opt/ebsofts/Compiler/GCCcore/4.9.3/zlib/1.2.8/lib are
I added
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/opt/ebsofts/Compiler/GCCcore/4.9.3/zlib/1.2.8/lib
at the beginning of the makefile, but still get the same error.
Issue the
export
command on the command line (don't add it to the makefile).Still the same error. But I tested on another account on the same cluster, and it worked perfectly. So the issue must be specifically related to my account. I will try to sort things out and post here what was wrong.
Many thanks for you help !