/home/software/MashMap/mashmap: error while loading shared libraries: libgsl.so.23: cannot open shared object file: No such file or directory

Question

/home/software/MashMap/mashmap: error while loading shared libraries: libgsl.so.23: cannot open shared object file: No such file or directory

Closed this issue 7 years ago · 12 comments

Please excuse my lack of informatics skills, but I'm having trouble with mashmap installation.
I'm using CentOS 7.3.1611 with gcc 4.8.5 20150623.
I installed gsl-2.4, then configured mashmap with:
$./bootstrap.sh
$./configure --with-gsl=/home/software/gsl-2.4/
$make
$/home/software/mashmap -s S15-132.contigs.fasta -q S15_132.1.subreads.fastq -o test1

Returns:
/home/software/MashMap/mashmap: error while loading shared libraries: libgsl.so.23: cannot open shared object file: No such file or directory

Answer 1 · 2017-08-15T16:10:44.000Z

I also removed the Mashmap directory and did a clean installation using the prefix:
./configure --prefix=/usr/local/ --with-gsl=/home/software/gsl-2.4/
make

It does not install the binary in /usr/local/bin/ (it installs in the Mashmap directory) and still give the same error as above.

BTW, I am performing the install as 'root'.

Answer 2 · 2017-08-18T20:13:19.000Z

Can you try --with-gsl=/home/software/gsl-2.4/build and see if it works?

Answer 3 · 2017-08-18T21:05:27.000Z

####Details below but that did not work.
####I removed the directory and did a fresh install:
[root@rambo software]# git clone https://github.com/marbl/MashMap.git
Cloning into 'MashMap'...
remote: Counting objects: 219, done.
remote: Compressing objects: 100% (8/8), done.
remote: Total 219 (delta 0), reused 3 (delta 0), pack-reused 211
Receiving objects: 100% (219/219), 120.90 KiB | 0 bytes/s, done.
Resolving deltas: 100% (115/115), done.
[root@rambo software]# cd MashMap/
[root@rambo MashMap]# ./bootstrap.sh
[root@rambo MashMap]# ./configure --with-gsl=/home/software/gsl-2.4/build
checking for g++... g++
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking how to run the C++ preprocessor... g++ -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking zlib.h usability... yes
checking zlib.h presence... yes
checking for zlib.h... yes
checking gsl/gsl_cdf.h usability... yes
checking gsl/gsl_cdf.h presence... yes
checking for gsl/gsl_cdf.h... yes
configure: creating ./config.status
config.status: creating Makefile
[root@rambo MashMap]# make
g++ -c -O3 -DNDEBUG -std=c++11 -Isrc -I /home/software/gsl-2.4/build/include -include src/common/memcpyLink.h -Wl,--wrap=memcpy -o src/map/mash_map.o src/map/mash_map.cpp
g++ -O3 -DNDEBUG -std=c++11 -Isrc -I /home/software/gsl-2.4/build/include -include src/common/memcpyLink.h -Wl,--wrap=memcpy src/map/mash_map.o -o mashmap -L/home/software/gsl-2.4/build/lib -lgsl -lgslcblas -lstdc++ -lz -lm -lpthread
[root@rambo MashMap]# ./mashmap
./mashmap: error while loading shared libraries: libgsl.so.23: cannot open shared object file: No such file or directory

####Tried adding frontslash at end of 'build'
[root@rambo MashMap]# cd ..
[root@rambo software]# rm -rf MashMap/
[root@rambo software]# git clone https://github.com/marbl/MashMap.git
Cloning into 'MashMap'...
remote: Counting objects: 219, done.
remote: Compressing objects: 100% (8/8), done.
remote: Total 219 (delta 0), reused 3 (delta 0), pack-reused 211
Receiving objects: 100% (219/219), 120.90 KiB | 0 bytes/s, done.
Resolving deltas: 100% (115/115), done.
[root@rambo software]# cd MashMap/
[root@rambo MashMap]# ./bootstrap.sh
[root@rambo MashMap]# ./configure --with-gsl=/home/software/gsl-2.4/build/
checking for g++... g++
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking how to run the C++ preprocessor... g++ -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking zlib.h usability... yes
checking zlib.h presence... yes
checking for zlib.h... yes
checking gsl/gsl_cdf.h usability... yes
checking gsl/gsl_cdf.h presence... yes
checking for gsl/gsl_cdf.h... yes
configure: creating ./config.status
config.status: creating Makefile
[root@rambo MashMap]# make
g++ -c -O3 -DNDEBUG -std=c++11 -Isrc -I /home/software/gsl-2.4/build//include -include src/common/memcpyLink.h -Wl,--wrap=memcpy -o src/map/mash_map.o src/map/mash_map.cpp
g++ -O3 -DNDEBUG -std=c++11 -Isrc -I /home/software/gsl-2.4/build//include -include src/common/memcpyLink.h -Wl,--wrap=memcpy src/map/mash_map.o -o mashmap -L/home/software/gsl-2.4/build//lib -lgsl -lgslcblas -lstdc++ -lz -lm -lpthread
[root@rambo MashMap]# ./mashmap -h
./mashmap: error while loading shared libraries: libgsl.so.23: cannot open shared object file: No such file or directory

Answer 4 · 2017-08-19T18:52:48.000Z

This should be because program is failing to find the gsl library in your library path at runtime.
In your environment file, you should update the variable LD_LIBRARY_PATH to include /home/software/gsl-2.4/build/lib

More details here.

Answer 5 · 2017-08-21T18:37:14.000Z

Hmm. My installation does not have a /build directory. I re-downloaded v2.4 and reinstalled with “./configure && make && make install” [root@rambo gsl-2.4]# ls aclocal.m4 config.h err gsl_nan.h INSTALL mkinstalldirs poly sum AUTHORS config.h.in fft gsl.pc install-sh monte qrng sys autogen.sh config.log fit gsl.pc.in integration multifit randist templates_off.h blas config.status gsl gsl_pow_int.h interpolation multifit_nlinear README templates_on.h block config.sub gsl-config gsl_precision.h libgsl.la multilarge rng test bspline configure gsl-config.in gsl-randist libtool multilarge_nlinear roots test-driver BUGS configure.ac gsl-histogram gsl-randist.c linalg multimin rstat test_gsl_histogram.sh build.h const gsl-histogram.c gsl-randist.o ltmain.sh multiroots siman THANKS cblas COPYING gsl-histogram.o gsl.spec Makefile multiset sort TODO cdf depcomp gsl_inline.h gsl.spec.in Makefile.am NEWS spblas utils ChangeLog deriv gsl.m4 gsl_types.h Makefile.in ntuple specfunc vector cheb dht gsl_machine.h gsl_version.h matrix ode-initval splinalg version.c combination diff gsl_math.h gsl_version.h.in mdate-sh ode-initval2 spmatrix version.lo complex doc gsl_minmax.h histogram min permutation stamp-h1 version.o config.guess eigen gsl_mode.h ieee-utils missing pkgconfig.test statistics wavelet From: Chirag Jain [mailto:notifications@github.com] Sent: Saturday, August 19, 2017 1:53 PM To: marbl/MashMap <MashMap@noreply.github.com> Cc: Waldbieser, Geoff <Geoff.Waldbieser@ARS.USDA.GOV>; Author <author@noreply.github.com> Subject: Re: [marbl/MashMap] /home/software/MashMap/mashmap: error while loading shared libraries: libgsl.so.23: cannot open shared object file: No such file or directory (#3) This should be because linker is failing to find the gsl library in your library path. In your environment file, you should update the LD_LIBRARY_PATH to include /home/software/gsl-2.4/build/lib More details here<https://www.gnu.org/software/gsl/manual/html_node/Shared-Libraries.html>. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub<#3 (comment)>, or mute the thread<https://github.com/notifications/unsubscribe-auth/ASb-Wmbgf87_Pom5hgUO7Vh6G0TyK1-Dks5sZy8AgaJpZM4O3wh5>. This electronic message contains information generated by the USDA solely for the intended recipients. Any unauthorized interception of this message or the use or disclosure of the information it contains may violate the law and subject the violator to civil or criminal penalties. If you believe you have received this message in error, please notify the sender and delete the email immediately.

Answer 6 · 2017-08-21T19:46:51.000Z

BTW, this is the Mashmap install but still have same result. [root@rambo MashMap]# ll total 24 -rwxr-xr-x. 1 root root 8 Aug 21 11:22 bootstrap.sh -rw-r--r--. 1 root root 1405 Aug 21 11:22 configure.ac -rw-r--r--. 1 root root 1665 Aug 21 11:22 INSTALL.txt -rw-r--r--. 1 root root 1540 Aug 21 11:22 LICENSE.txt -rw-r--r--. 1 root root 744 Aug 21 11:22 Makefile.in -rw-r--r--. 1 root root 3498 Aug 21 11:22 README.md drwxr-xr-x. 2 root root 36 Aug 21 11:22 scripts drwxr-xr-x. 4 root root 41 Aug 21 11:22 src [root@rambo MashMap]# ./bootstrap.sh [root@rambo MashMap]# ./configure --with-gsl=/home/software/gsl-2.4/build checking for g++... g++ checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking how to run the C++ preprocessor... g++ -E checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking zlib.h usability... yes checking zlib.h presence... yes checking for zlib.h... yes checking gsl/gsl_cdf.h usability... yes checking gsl/gsl_cdf.h presence... yes checking for gsl/gsl_cdf.h... yes configure: creating ./config.status config.status: creating Makefile [root@rambo MashMap]# make g++ -c -O3 -DNDEBUG -std=c++11 -Isrc -I /home/software/gsl-2.4/build/include -include src/common/memcpyLink.h -Wl,--wrap=memcpy -o src/map/mash_map.o src/map/mash_map.cpp g++ -O3 -DNDEBUG -std=c++11 -Isrc -I /home/software/gsl-2.4/build/include -include src/common/memcpyLink.h -Wl,--wrap=memcpy src/map/mash_map.o -o mashmap -L/home/software/gsl-2.4/build/lib -lgsl -lgslcblas -lstdc++ -lz -lm –lpthread From: Chirag Jain [mailto:notifications@github.com] Sent: Saturday, August 19, 2017 1:53 PM To: marbl/MashMap <MashMap@noreply.github.com> Cc: Waldbieser, Geoff <Geoff.Waldbieser@ARS.USDA.GOV>; Author <author@noreply.github.com> Subject: Re: [marbl/MashMap] /home/software/MashMap/mashmap: error while loading shared libraries: libgsl.so.23: cannot open shared object file: No such file or directory (#3) This should be because linker is failing to find the gsl library in your library path. In your environment file, you should update the LD_LIBRARY_PATH to include /home/software/gsl-2.4/build/lib More details here<https://www.gnu.org/software/gsl/manual/html_node/Shared-Libraries.html>. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub<#3 (comment)>, or mute the thread<https://github.com/notifications/unsubscribe-auth/ASb-Wmbgf87_Pom5hgUO7Vh6G0TyK1-Dks5sZy8AgaJpZM4O3wh5>. This electronic message contains information generated by the USDA solely for the intended recipients. Any unauthorized interception of this message or the use or disclosure of the information it contains may violate the law and subject the violator to civil or criminal penalties. If you believe you have received this message in error, please notify the sender and delete the email immediately.

Answer 7 · 2017-08-21T20:58:51.000Z

Mashmap executable is not able to find the libgsl library. It is usually searched in the paths specified by the LD_LIBRARY_PATH environment variable. When you install gsl, it should generate the build libraries for you.

Answer 8 · 2017-08-21T21:02:16.000Z

Yes, I understand. So apparently gsl is not installing properly since it does not produce a /build directory. I will try releases earlier than v2.4.

Answer 9 · 2017-08-21T21:05:38.000Z

Or it may be placing the libraries in some other directory. I am not sure what the default location is, perhaps /usr/local/lib?

Answer 10 · 2017-08-21T21:24:50.000Z

Yes, they're in /usr/local/lib/ and I have tried to point to that during configuration and it seems happy to find the libraries there.
...
[root@rambo Mashmap]$./bootstrap.sh
[root@rambo Mashmap]$./configure --with-gsl=/usr/local/lib

checking gsl/gsl_cdf.h usability... yes
checking gsl/gsl_cdf.h presence... yes
checking for gsl/gsl_cdf.h... yes
configure: creating ./config.status
config.status: creating Makefile

[root@rambo Mashmap]$make
[root@rambo Mashmap]$ ./mashmap
./mashmap: error while loading shared libraries: libgsl.so.19: cannot open shared object file: No such file or directory

###Here are the libraries in /usr/local/lib/
[root@rambo lib]$ ll libgsl*
-rw-r--r--. 1 root root 19081320 Aug 21 16:11 libgsl.a
-rw-r--r--. 1 root root 1757170 Aug 21 16:11 libgslcblas.a
-rwxr-xr-x. 1 root root 949 Aug 21 16:11 libgslcblas.la
lrwxrwxrwx. 1 root root 20 Aug 21 16:11 libgslcblas.so -> libgslcblas.so.0.0.0
lrwxrwxrwx. 1 root root 20 Aug 21 16:11 libgslcblas.so.0 -> libgslcblas.so.0.0.0
-rwxr-xr-x. 1 root root 1047600 Aug 21 16:11 libgslcblas.so.0.0.0
-rwxr-xr-x. 1 root root 918 Aug 21 16:11 libgsl.la
lrwxrwxrwx. 1 root root 16 Aug 21 16:11 libgsl.so -> libgsl.so.19.3.0
lrwxrwxrwx. 1 root root 16 Aug 21 16:11 libgsl.so.19 -> libgsl.so.19.3.0
-rwxr-xr-x. 1 root root 11293856 Aug 21 16:11 libgsl.so.19.3.0

Answer 11 · 2017-09-17T20:22:31.000Z

Is /usr/local/lib in LD_LIBRARY_PATH? What does echo $LD_LIBRARY_PATH report?

Answer 12 · 2017-09-19T16:21:23.000Z

We upgraded the machine to contain larger HDDs so I reinstalled CentOS 7 and reinstalled the software. LD_LIBRARY_PATH was empty. After adding :/usr/lib to LD_LIBRARY_PATH then Mashmap works. Thank you. From: Sergey Koren [mailto:notifications@github.com] Sent: Sunday, September 17, 2017 3:23 PM To: marbl/MashMap <MashMap@noreply.github.com> Cc: Waldbieser, Geoff <Geoff.Waldbieser@ARS.USDA.GOV>; Author <author@noreply.github.com> Subject: Re: [marbl/MashMap] /home/software/MashMap/mashmap: error while loading shared libraries: libgsl.so.23: cannot open shared object file: No such file or directory (#3) Is /usr/local/lib in LD_LIBRARY_PATH? What does echo $LD_LIBRARY_PATH report? — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub<#3 (comment)>, or mute the thread<https://github.com/notifications/unsubscribe-auth/ASb-WmQS7OxVDPh1pA2yGJuVqOGNI4AIks5sjX-IgaJpZM4O3wh5>. This electronic message contains information generated by the USDA solely for the intended recipients. Any unauthorized interception of this message or the use or disclosure of the information it contains may violate the law and subject the violator to civil or criminal penalties. If you believe you have received this message in error, please notify the sender and delete the email immediately.