Since a few days I get the following error when I try to open python that was installed with conda. The only thing that changed is that I changed the group of the files located in /software and gave the group read and write writes.
/software/local/share/bcbio/anaconda/bin/python: error while loading shared libraries: libpython2.7.so.1.0: cannot open shared object file: No such file or directory
I tried many different things. I first look at the output of ldd
ldd /software/local/share/bcbio/anaconda/bin/python
linux-vdso.so.1 => (0x00007ffd11bfc000)
libpython2.7.so.1.0 => /software/local/share/bcbio/anaconda/bin/../lib/libpython2.7.so.1.0 (0x00007f276fa9b000)
libpthread.so.0 => /lib64/libpthread.so.0 (0x00000036be600000)
libdl.so.2 => /lib64/libdl.so.2 (0x00000033bd800000)
libutil.so.1 => /lib64/libutil.so.1 (0x00000033bec00000)
libm.so.6 => /lib64/libm.so.6 (0x00000033be000000)
libc.so.6 => /lib64/libc.so.6 (0x00000033bd400000)
/lib64/ld-linux-x86-64.so.2 (0x00000033bd000000)
And looked at the permission of the librarie, which seemed to be correct:
ls -lah /software/local/share/bcbio/anaconda/bin/../lib/libpython2.7.so.1.0
-rwxrwsr-x+ 1 vsc lp_neuro 7.7M Jun 7 2018 /software/local/share/bcbio/anaconda/bin/../lib/libpython2.7.so.1.0
I also tried to export different environment variables:
export LD_LIBRARY_PATH=/software/local/share/bcbio/anaconda/bin/../lib/;
export PYTHONHOME=/software/local/share/bcbio/anaconda/bin/../lib/;
export PYTHONPATH=/software/local/share/bcbio/anaconda/bin/../lib/;
Since it is a conda installation of python, solutions needing root access (which I do not have) are of no uses. E.g. editing /etc/ld.so.conf is no option for me.
Is there a way to fix this issue?
Related
I have built and installed DPDK v.18.11.9 on Centos 7 using x86_64-native-linuxapp-gcc and option:
CONFIG_RTE_BUILD_SHARED_LIB=y
We want to run testpmd but it fails to load:
$ ./x86_64-native-linuxapp-gcc/app/testpmd
./x86_64-native-linuxapp-gcc/app/testpmd: error while loading shared
libraries: librte_pmd_bond.so.2.1: cannot open shared object file: No such file or directory
This is expected as lib/ does not contain librte_pmd_bond.so.
What build options should I use to build this library?
Best regards
David
This is a common error when one forgets to point the application elf the path for libraries. When DPDK libraries are built with shared mode, one has to specify the path to dpdk shared object via LD_LIBRARY_PATH. In failing to do so we get
# ldd app/testpmd
linux-vdso.so.1 (0x00007fff3eeb2000)
librte_pmd_bond.so.2.1 => not found
librte_pmd_dpaa.so.1.1 => not found
librte_pmd_ixgbe.so.2.1 => not found
librte_pmd_i40e.so.2.1 => not found
librte_pmd_bnxt.so.2.1 => not found
librte_pmd_softnic.so.1.1 => not found
librte_pdump.so.2.1 => not found
librte_metrics.so.1.1 => not found
librte_bitratestats.so.2.1 => not found
librte_latencystats.so.1.1 => not found
librte_bpf.so.1.1 => not found
librte_gro.so.1.1 => not found
librte_gso.so.1.1 => not found
librte_mbuf.so.4.1 => not found
librte_net.so.1.1 => not found
librte_ethdev.so.11.1 => not found
librte_mempool.so.5.1 => not found
librte_ring.so.2.1 => not found
librte_eal.so.9.1 => not found
librte_cmdline.so.2.1 => not found
libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f1474089000)
libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f1473c98000)
/lib64/ld-linux-x86-64.so.2 (0x00007f14745cf000)
Thereby running the application we get
# ./app/testpmd
./app/testpmd: error while loading shared libraries: librte_pmd_bond.so.2.1: cannot open shared object file: No such file or directory
To fix the error, as mentioned above use
export LD_LIBRARY_PATH=[path to dpdk shared libraries]
this resolves the dependencies and application runs.
I'm developing an C++ application under Ubuntu 16 using google protobuf. When I compile and run at the same machine, it works fine, but when I try to run it at another Ubuntu 16 I get the following error
./APP: Symbol `_ZTVN6google8protobuf11MessageLiteE' has different size in shared object, consider re-linking
./APP: Symbol `_ZTVN6google8protobuf7MessageE' has different size in shared object, consider re-linking
If I compile the same source at this second machine it works fine, but if I run at the first machine, I get the error too.
I tried to copy all the libraries listed with ldd to an path at the other machine and I user the export LD_LIBRARY_PATH, and not working too.
ldd result at both machines are the same.
linux-vdso.so.1 => (0x00007ffd40fda000)
libsqlite3.so.0 => /usr/lib/x86_64-linux-gnu/libsqlite3.so.0 (0x00007f011b4b3000)
libzmq.so.5 => /usr/lib/x86_64-linux-gnu/libzmq.so.5 (0x00007f011b24d000)
libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f011b030000)
libprotobuf.so.22 => /usr/local/lib/libprotobuf.so.22 (0x00007f011ab87000)
libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6 (0x00007f011a805000)
libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007f011a5ef000)
libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f011a225000)
libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007f011a021000)
libsodium.so.18 => /usr/lib/x86_64-linux-gnu/libsodium.so.18 (0x00007f0119dc3000)
librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00007f0119bbb000)
/lib64/ld-linux-x86-64.so.2 (0x00007f011b788000)
libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f01198b2000)
In Ubuntu 15.04 64 bits I installed Qt5.6 (online installer) and while trying to move my development environment from Windows 7 to Linux I faced the following:
SqlDatabase: QMYSQL driver not loaded
Following this, I managed to find ~/Qt/5.6/gcc_64/plugins/sqldrivers/libqsqlmysql.so and then:
$ ldd libqsqlmysql.so
linux-vdso.so.1 => (0x00007ffffd571000)
libmysqlclient_r.so.16 => not found
libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x00007fe94ef24000)
libcrypt.so.1 => /lib/x86_64-linux-gnu/libcrypt.so.1 (0x00007fe94ecec000)
libnsl.so.1 => /lib/x86_64-linux-gnu/libnsl.so.1 (0x00007fe94ead2000)
libssl.so.10 => not found
libcrypto.so.10 => not found
libQt5Sql.so.5 => /home/user/Qt/5.6/gcc_64/plugins/sqldrivers/../../lib/libQt5Sql.so.5 (0x00007fe94e88d000)
libQt5Core.so.5 => /home/user/Qt/5.6/gcc_64/plugins/sqldrivers/../../lib/libQt5Core.so.5 (0x00007fe94e17a000)
libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007fe94df5c000)
libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6 (0x00007fe94dc4d000)
libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007fe94d944000)
libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007fe94d72e000)
libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007fe94d364000)
libicui18n.so.56 => /home/user/Qt/5.6/gcc_64/plugins/sqldrivers/../../lib/libicui18n.so.56 (0x00007fe94cec9000)
libicuuc.so.56 => /home/user/Qt/5.6/gcc_64/plugins/sqldrivers/../../lib/libicuuc.so.56 (0x00007fe94cb11000)
libicudata.so.56 => /home/user/Qt/5.6/gcc_64/plugins/sqldrivers/../../lib/libicudata.so.56 (0x00007fe94b12e000)
libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007fe94af29000)
libgthread-2.0.so.0 => /usr/lib/x86_64-linux-gnu/libgthread-2.0.so.0 (0x00007fe94ad27000)
librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00007fe94ab1f000)
libglib-2.0.so.0 => /lib/x86_64-linux-gnu/libglib-2.0.so.0 (0x00007fe94a80f000)
/lib64/ld-linux-x86-64.so.2 (0x000056024837f000)
libpcre.so.3 => /lib/x86_64-linux-gnu/libpcre.so.3 (0x00007fe94a5a2000)
Tells libmysqlclient_r.so.16 => not found. In fact, it seems I have a newer version:
find / -name libmysqlclient_r*
/usr/lib/x86_64-linux-gnu/libmysqlclient_r.so.18
/usr/lib/x86_64-linux-gnu/libmysqlclient_r.so.18.1.0
/usr/lib/x86_64-linux-gnu/libmysqlclient_r.so
/usr/lib/x86_64-linux-gnu/libmysqlclient_r.a
Perhaps that's the problem. Could some one confirm? How should I proceed?
First and foremost, double check that you have the packages containing libssl.so, libcrypto.so and libmysqlclient_r.so installed (looks like you have this last one, it's extremely likely you also have the first two, but just double check).
Then, your problem is that you have those shared objects with a different SONAME, sign that they're binary incompatible with the plugin shipped with Qt, which therefore needs to be recompiled.
Therefore:
install the development versions of the packages found above (libssl-dev, mysql-client-dev or similar).
run the MaintenanceTool from your Qt installation, and be sure to select to install Qt's source code too.
Go in QTDIR/5.6/Src/qtbase/src/plugins/sqldrivers/mysql/.
Run the right qmake, i.e. the one coming from that installation of Qt (not the system wide one or similar). Best way to be sure is providing the full path to it: QTDIR/5.6/gcc_64/bin/qmake.
Run make. Hopefully this will just workâ˘; if it complains about some missing libraries, install them and rerun make.
This should now have produced a new libqsqlmysql.so plugin; overwrite the old one with this new one.
I am using Ubuntu 18.04.4 and compiling my project using system's Qt5. The driver is successfully loaded after I install libqt5sql5-mysql package.
sudo apt-get install libqt5sql5-mysql
There are two fixes for this issue. First try and locate the qtbase folder located within your qt directory and try run ./configure -plugin-sql-mysql which will activate the driver if they're missing.
If this doesn't solve your issue, I suggest that you double check your code and try running one of the Qt examples which makes a connection to the Sql databases. I.e. modify the example code which connects to a local SQLite database changing the parameter to MySQL. If this example doesn't throw 'Driver not loaded error' then follow the step below.
Make sure you're using the static function of the QSqlDatabase i.e. rather than using
QSqlDatabase *db = new QSqlDatabase();
db->addDatabase("QMYSQL");
you should be doing
QSqlDatabase db = QSqlDatabase::addDatabase("QMYSQL");
I also have the same problem with Qt5.11.1 and my OS is Ubuntu16.04 and I have resolve the problem by installing libmysqlclient18 from here
https://launchpad.net/ubuntu/xenial/amd64/libmysqlclient18/5.6.25-0ubuntu1
After download run the command from download directory,
sudo dpkg -i libmysqlclient18_5.6.25-0ubuntu1_amd64.deb
For use MySql with PyQt5 on Raspberry Pi, it's fine to install:
sudo apt-get install libqt5sql5-mysql
and
sudo apt-get install libqt5sql5-mysql
When I run my Fortran code under Ubuntu 14.04 OS I get the following error:error while loading shared libraries: libnetcdff.so.6: cannot open shared object file: No such file or directory. I saw the ld path with ldd KiD_SC_2D.exe but it seems that libnetcdff is found:
beata#beata-HP-Z420-Workstation:~/Downloads/kid_a_setup/bin$ ldd KiD_SC_2D.exe
linux-vdso.so.1 => (0x00007fffd83a4000)
libnetcdff.so.6 => /home/beata/netcdf/lib/libnetcdff.so.6 (0x00007f3849432000)
libgfortran.so.3 => /usr/lib/x86_64-linux-gnu/libgfortran.so.3 (0x00007f3849101000)
libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f3848dfa000)
libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007f3848be4000)
libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f384881f000)
libnetcdf.so.7 => /home/beata/netcdf/lib/libnetcdf.so.7 (0x00007f3848533000)
libquadmath.so.0 => /usr/lib/x86_64-linux-gnu/libquadmath.so.0 (0x00007f38482f7000)
/lib64/ld-linux-x86-64.so.2 (0x00007f3849694000)
When I had run gdb I got the following warning:
warning: the debug information found in "/lib64/ld-2.19.so" does not match "/lib64/ld-linux-x86-64.so.2" (CRC mismatch)
Is it possible that this warning causes the matter of libnetcdff.so.6? As so how I can fix this CRC mismatch?
Is it possible that this warning causes the matter of libnetcdff.so.6?
No, it's entirely unrelated.
As so how I can fix this CRC mismatch?
The mismatch says that the installed version of libc6 and libc6-dbg packages do not match. Update libc6-dbg to match installed libc6, and the warning should go away.
As for why libnetcdff.so.6 is not found, you are not telling us the whole story. Clearly ldd does find it, and running KiD_SC_2D.exe should as well. To debug this, you may wish to run it like so:
cd ~/Downloads/kid_a_setup/bin
env LD_DEBUG=files,libs ./KiD_SC_2D.exe
That should tell you where the dynamic linker is looking for libnetcdff.
I am using Debian (which comes with Python-2.7.3), trying to compile Python-2.7.6 from source for use with mod_wsgi alongside Apache.
Apparently you must use --enable-shared when compiling for mod_wsgi usage, according to numerous answers.
Following these steps:
./configure --enable-shared --prefix=/usr/local/bin/python-2.7.6
make
make install
And then checking the interactive shell #
/usr/local/bin/python-2.7.6/bin/python
I am greeted with "Python 2.7.3 (default, Jan 2 2013, 14:09:21)" etc
Why is it resulting in Python 2.7.3?
I tried ldd against the executable and this is the result:
linux-vdso.so.1 => (0x00007fff271ff000)
libpython2.7.so.1.0 => /usr/lib/libpython2.7.so.1.0 (0x00007f1545638000)
libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f154541c000)
libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007f1545217000)
libutil.so.1 => /lib/x86_64-linux-gnu/libutil.so.1 (0x00007f1545014000)
libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f1544d92000)
libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f1544a06000)
libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x00007f15447ef000)
libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007f15445d9000)
/lib64/ld-linux-x86-64.so.2 (0x00007f1545b40000)
How do I stop it from using the system library and instead use the locally compiled version?
I know that it is a lot easier for me to just revert to using the system installed Python version, and that the real-world difference is zero. But this behaviour seems strange.
When you do the make of Python, run it as:
LD_RUN_PATH=/usr/local/lib make
Setting the environment variable LD_RUN_PATH forces 'python' executable generated to look in /usr/local/lib before /usr/lib for Python shared library.
This is mentioned in the mod_wsgi documentation.
http://code.google.com/p/modwsgi/wiki/CheckingYourInstallation#Python_Shared_Library
Before doing this again, make sure you do a 'make distclean' and rerun configure to make sure you haven't got old build products around.