I am trying to get CUDA5 to work on a shared cluster.
When I invoke the local gcc to build large applications it works just fine. When I use the CUDA wrapper I get an error saying that it can't find certain parts of glib.
Why is CUDA looking at /lib64/libc.so.6, if I specified the local gcc library directory?
[uid002#n001 cuda5test]$ ldd /home/ex/uid002/cuda/lib64/libcudart.so
/home/ex/uid002/cuda/lib64/libcudart.so: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /home/ex/uid002/cuda/lib64/libcudart.so)
linux-vdso.so.1 => (0x00007fff277ff000)
libdl.so.2 => /lib64/libdl.so.2 (0x00007f5328da6000)
libpthread.so.0 => /lib64/libpthread.so.0 (0x00007f5328b89000)
librt.so.1 => /lib64/librt.so.1 (0x00007f5328981000)
libstdc++.so.6 => /home/ex/uid002/gcc/lib64/libstdc++.so.6 (0x00007f532867d000)
libm.so.6 => /lib64/libm.so.6 (0x00007f53283f8000)
libgcc_s.so.1 => /home/ex/uid002/gcc/lib64/libgcc_s.so.1 (0x00007f53281e3000)
libc.so.6 => /lib64/libc.so.6 (0x00007f5327e67000)
/lib64/ld-linux-x86-64.so.2 (0x000000335ae00000)
And
[uid002#n001 cuda5test]$ echo $LD_LIBRARY_PATH
/home/ex/uid002/cuda/lib64:/home/ex/uid002/gmp/lib:/home/ex/uid002/mpfr/lib:/home/ex/uid002/mpc/lib:/home/ex/uid002/gcc/lib64
I have tried to reinstall the CUDA package, and this was no help.
libcudart.so: /lib64/libc.so.6: version `GLIBC_2.14' not found
This error means that the libcudart.so library was linked on a system with glibc-2.14 or later. You can only use that library if your system (both at link time and at runtime) has glibc version >= 2.14. Your system does not satisfy prerequisite for libcudart.so. You'll have to use older version of libcudart.so, or upgrade your system.
(Be careful: upgrading glibc incorrectly is a sure way to render the system un-bootable.)
Why is CUDA looking at /lib64/libc.so.6, if I specified the local gcc library directory?
Glibc is not part of GCC distribution, and is completely independent. "local gcc library directory" is unlikely to have libc.so in it.
Related
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?
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 work™; 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
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 work™; 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.