I am trying to install gcc version 12.2.0 (as super user $ sudo su) using SPACK $ spack install gcc#12.2.0. Nothing happend but the following error message: ==> Error: Package 'apple-gl' not found
How can I update or obtain this "apple-gl" package?
Btw, I do have opengl installed, but I can not update neither via anaconda nor spack the opengl library up to date
$ apt-cache search opengl
gir1.2-mutter-6 - GObject introspection data for Mutter
libcogl-common - Object oriented GL/GLES Abstraction/Utility Layer (common files)
libcogl-dev - Object oriented GL/GLES Abstraction/Utility Layer (development files)
libcogl-doc - Object oriented GL/GLES Abstraction/Utility Layer (documentation)
libcogl-pango-dev - Object oriented GL/GLES Abstraction/Utility Layer (development files)
libcogl-pango20 - Object oriented GL/GLES Abstraction/Utility Layer
...
Could this be caused by using multiple versions of Spack and sharing the misc
cache directory? I have seen this when updating the Spack version.
You can clear the misc cache by running the command:
spack clean --misc-cache
I've been bitten by the misc cache a few times so I usually add a misc_cache entry to config.yaml and set the path to be version specific.
Related
Really basic issue. I'm trying to install the Datastax Cassandra C++ driver on my Ubuntu 16.0.4 machine. It really shouldn't be that difficult. I've installed all dependencies using dpkg and installed the cassandra driver deb file. But I can't find (or #include) the cassandra.h file.
Running
$ locate cassandra.h
returns nothing and running
$ locate cassandra*
returns a whole mess of files from cqlsh, the casssandra config files, etc, but no header files for the cpp driver.
Additionally, cassandra-cpp-driver doesn't show up in dpkg -l (though apt-get and dpkg -i say it's already installed).
Any help getting this installed would be appreciated.
DataStax C/C++ Driver for Apache Cassandra is currently not available from the Ubuntu official repository.
There are .deb packages for Ubuntu which are available as mentioned in the DataStax project documentation on github datastax/cpp-driver repository from this location:
http://downloads.datastax.com/cpp-driver/
If you are using Ubuntu 16.04, the last .deb available are under ubuntu/16.04/cassandra/v2.7.0/.
You will find the cassandra.h file in cassandra-cpp-driver-dev_2.7.0-1_amd64.deb, which you need to download and install with dpkg.
The suffix dev in a Debian or Ubuntu package denotes a package meant for developing programs, containing, in particular, header files.
dpkg -i cassandra-cpp-driver-dev_2.7.0-1_amd64.deb
The header will get installed in the usual location under Linux for header files that your compiler should find without a problem: /usr/include/cassandra.h.
it will also install:
/usr/lib/x86_64-linux-gnu/libcassandra_static.a
/usr/lib/x86_64-linux-gnu/pkgconfig/cassandra.pc
/usr/lib/x86_64-linux-gnu/pkgconfig/cassandra_static.pc
/usr/share/doc/cassandra-cpp-driver-dev/changelog.Debian.gz
/usr/share/doc/cassandra-cpp-driver-dev/copyright
which you will need for static linking and for pkgconfig to work properly.
What you may have installed is cassandra-cpp-driver_2.7.0-1_amd64.deb which contains the libcassandra.so.2.7.0 that is the shared object (dynamic) library binary file,.. although whatever you installed should indeed come in the result of a dkpg -l query such as:
dpkg -l | grep cassandra
If you installed anything from an unofficial source, I would suggest you uninstall these first, and install the provided .deb for your plaform from the official source.
Follow the documentation's instructions for making your first program with this library.
To give as much background as possible -
I have a machine learning model trained using keras i'm trying to embed on an nvidia jetson tx2.
I have set up tensorflow on there (a bit of a pain in itself) however when i run my script i'm hitting an error with protobuf.
Using TensorFlow backend.
[libprotobuf FATAL google/protobuf/stubs/common.cc:61] This program requires version 3.1.0 of the Protocol Buffer runtime library, but the installed version is 2.6.1. Please update your library. If you compiled the program yourself, make sure that your headers are from the same version of Protocol Buffers as your link-time library. (Version verification failed in "external/protobuf/src/google/protobuf/any.pb.cc".)
terminate called after throwing an instance of 'google::protobuf::FatalException'
what(): This program requires version 3.1.0 of the Protocol Buffer runtime library, but the installed version is 2.6.1. Please update your library. If you compiled the program yourself, make sure that your headers are from the same version of Protocol Buffers as your link-time library. (Version verification failed in "external/protobuf/src/google/protobuf/any.pb.cc".)
Aborted (core dumped)
So - i upgraded protobuf using pip at first but i thought the clash is because c++ version is taking priority and the version in linux was still stating 2.6.1 however after building in c++ the version is now shown as 3.1.0 however i am still getting the same error.
From the nvidia dev forums i received some feedback
"/usr/lib/aarch64-linux-gnu/libprotobuf.so.9.0.1
This means that C/C++ code will find version 2.6.
pip install protobuf-3.1.0-py2.py3-none-any.whl
This means that Python code will find version 3.1.
You need to upgrade the C++ (system) library to match version 3.1.
I don't think there's a default package on Ubuntu that does this, so you will have to either hack it by building your own and installing it on top of the system package, or you will have to find a deb package that has a newer version that will still install on your current system."
Ive really been struggling with this as i cant find a way to upgrade the system files. Any help would be much appreciated
Thanks
edit: i'm also wondering could this be a clash with GTK (i am also using openCV here so thats worth a mention!)
Please check your version of libprotobuf-dev.
Please try to uninstall your existing one on your PC with following commands:
apt-get remove --purge libprotobuf-dev
Then, build new version of libprotobuf-dev:
apt-get install autoconf automake libtool curl make g++ unzip
wget https://github.com/google/protobuf/releases/download/v3.5.0/protobuf-cpp-3.5.0.tar.gz
tar -xvf protobuf-cpp-3.5.0.tar.gz
cd protobuf-3.5.0
./autogen.sh
./configure
make
make check
sudo make install
sudo ldconfig
Good luck.
References:
https://github.com/BVLC/caffe/issues/5711
https://github.com/google/protobuf/issues/2979
step 1:
first, uninstall with purge protobuf
sudo apt-get remove --purge libprotobuf
step 2:
start a fresh one
$ wget https://raw.githubusercontent.com/jkjungavt/jetson_nano/master/install_protobuf-3.6.1.sh
sudo chmod +x install_protobuf-3.6.1.sh
./install_protobuf-3.6.1.sh #this time will take 30 min on my board.
I want to build static Rust executables with a customized version of musl. As a first step, I'm making myself familiar with Rust's build system.
I took the slightly outdated docker-rust-musl GitHub project and updated URLs that went out-of-date. Everything seems to work well with the build, but when I want to compile with x86_64-unknown-linux-musl the compiler doesn't find the musl std crate:
root#beb234fba4af:/build# cat example.rs
fn main() { println!("hi!"); panic!("failed"); }
root#beb234fba4af:/build# rustc --target=x86_64-unknown-linux-musl example.rs
error[E0463]: can't find crate for `std`
|
= note: the `x86_64-unknown-linux-musl` target may not be installed
error: aborting due to previous error
In fact, /usr/local/lib/rustlib/ only contains the x86_64-unknown-linux-gnu directory, even though output during the build indicates that x86_64-unknown-linux-musl is built:
[...]
Building stage2 std artifacts (x86_64-unknown-linux-gnu -> x86_64-unknown-linux-musl)
[...]
However, when it comes to the installation step x86_64-unknown-linux-gnu is nowhere to be seen:
[...]
Install std stage2 (x86_64-unknown-linux-gnu)
install: creating uninstall script at /usr/local/lib/rustlib/uninstall.sh
install: installing component 'rust-std-x86_64-unknown-linux-gnu'
std is standing at the ready.
Install rustc stage2 (x86_64-unknown-linux-gnu)
install: creating uninstall script at /usr/local/lib/rustlib/uninstall.sh
install: installing component 'rustc'
Rust is ready to roll.
Build completed in 0:31:07
What do I have to do to install the x86_64-unknown-linux-musl Rust standard library?
Progress:
Digging through the build environment revealed that make all builds the Rust std library with musl but the subsequent make install step does not install it.
We have a temporary fix in the build.sh script of the previously mentioned docker image.
It is unclear whether that is an issue of the build environment or of its usage.
The issue is known to the Rust developers. No eta of the fix, however.
I am trying to build from source for RedHawk installation and trying to replace uhd3.5.3 with a higher version of uhd for USRP_UHD module. I saw USRP_UHD source code, but found nowhere for uhd3.5.3 source code. I am guessing it might simply use "yum install ..." to download and install uhd host code and suporting libraries. Does anybody know where this code is located in redhawk_src_2.0 package? Or is there an efficient way in linux to search for this among all the files in redhawk_src_2.0 package?
Thanks in advance!
UHD is the USRP Harware driver softwware from Ettus Research. The UHD is distributed from:
http://files.ettus.com/binaries/uhd_stable/
Version 3.5.3 is here:
http://files.ettus.com/binaries/uhd_stable/uhd_003.005.003-release/
The current release is 3.9.2:
http://files.ettus.com/binaries/uhd_stable/uhd_003.009.002-release/
Hopefully this helps. I wasn't 100% sure what you are asking for.
First, clone the uhd library:
git clone git://github.com/EttusResearch/uhd.git
Then checkout the 3.9.2 tag:
git checkout release_003_009_002
Using the instructions from Ettus (http://files.ettus.com/manual/page_build_guide.html), install the dependencies listed under the Fedora section:
sudo yum -y install boost-devel libusb1-devel python-mako doxygen python-docutils cmake make gcc gcc-c++
Next, generate the Makefiles with CMake:
cd <uhd-repo-path>/host
mkdir build
cd build
cmake -DCMAKE_INSTALL_PREFIX=/opt/uhd ../
I recommend using an alternate install prefix at first to preserve the 3.5.3 version, just in case, but if you don't want to, just run:
cmake ../
instead of the longer command with the -DCMAKE_INSTALL_PREFIX flag. (Note: I couldn't get cmake to find the installed boost version, so you may have to do some other research on that since it is probably a whole different stackoverflow post in and of itself)
Now build and install the uhd library:
make
make test
sudo make install
Now that the library is installed, you should edit the USRP_UHD/cpp/configure.ac so that the PKG_CONFIG_PATH points to your install prefix (either the one specified in the flag above, or if you did the default, just leave it, as it should already be pointing to /usr/local/lib/pkgconfig). Also in the configure.ac file, make sure to change the uhd version number to 3.9.2.
Now you should be able to rebuild the USRP_UHD Device:
./reconf && ./configure && make install
I don't guarantee that the Device will build against the new version of the uhd library, that will depend on what (if anything) has been deprecated an removed from the library between the supported version and the newest one.
Finally, if you get through all of those steps successfully and if you specified a non-standard install prefix, you will have to add this prefix to either the LD_LIBRARY_PATH or an /etc/ld.so.conf.d/ script in order for the Device to correctly execute.
Clarification - you can follow the Redhawk manual appendix B for building Redhawk from source AFTER installing UHD v3.9.3 from source as per pwolframs instructions. The UHD v3.5.3 is not packaged with the Redhawk source code, only the Redhawk RPM, disregard all those RPMs when building UHD and Redhawk from source.
I am tearing my hair out trying to install Spatialite for GeoDjango!
I am already using Homebrew, it's generally easy and convenient so I initially tried to follow the Homebrew instructions for GeoDjango.
But this stops short of installing any database, i.e. Spatialite. The next step is to try and install Spatialite itself, but there are no Homebrew-specific instructions provided by Django docs.
I found this tutorial which looks perfect - a Homebrew and virtualenv-friendly install of Spatialite for GeoDjango.
But it doesn't work... it appears that my pysqlite is linked against the non-spatial-enabled version of SQLite that comes with OS X, rather than the Spatial-ised one I installed from Homebrew, I get this error when Django tried to connect to the db:
"The pysqlite library does not support C extension loading. Both SQLite and pysqlite must be configured to allow the loading of extensions to use SpatiaLite."
The author of pysqlite hasn't responded to my pleas for help on Github and I haven't found anything via Google.
So I went back to the drawing board and decided to follow the "Mac OS X-specific instructions" in the GeoDjango docs... by installing the various geo libs from the KyngChaos binary packages.
The docs say "Install the packages in the order they are listed above" but I found I couldn't install UnixImageIO without installing PROJ first. The link in the docs to download Spatialite binaries (http://www.gaia-gis.it/spatialite-2.3.1/binaries.html) is broken so I used the "Spatialite Tools v4.1" from KyngChaos instead.
Proceeding to the next step I get this error:
$ spatialite geodjango.db "SELECT InitSpatialMetaData();"
SQLite header and source version mismatch
2013-10-17 12:57:35 c78be6d786c19073b3a6730dfe3fb1be54f5657a
2013-09-03 17:11:13 7dd4968f235d6e1ca9547cda9cf3bd570e1609ef
Not really sure what's wrong at this point.
There is someone else here on SO who has gone the KyngChaos route and just ends up with the same "Both SQLite and pysqlite must be configured to allow the loading of extensions" error I got from the Homebrew route anyway.
I found this ticket #17756 for adding pyspatialite support to Django - pyspatialite is supposed to be an easier way to pip install everything but unfortunately it doesn't work either (see comments towards bottom of ticket).
I'm a bit reluctant to start trying to build everything from source by hand as it seems likely I'll just run into the same problems again, but spending hours Googling for info about cryptic compiler errors, magic flags and paths etc along the way.
I'm about ready to give up and just use Postgres/PostGIS.
I was able to get this working now, using the tip here:
https://github.com/ghaering/pysqlite/issues/60#issuecomment-50345210
I'm not sure if it was using the real paths that fixed it, or just the Homebrew kegs or underlying packages have been updated and now install cleanly. Still, it works now.
I reproduce below the steps I took:
brew update
brew install sqlite # 3.8.5
brew install libspatialite # 4.2.0
brew install spatialite-tools # 4.1.1
git clone https://github.com/ghaering/pysqlite.git
cd pysqlite
(where brew reported I had existing versions I unlinked them and installed the latest as commented above)
then edited setup.cfg to comment out #define=SQLITE_OMIT_LOAD_EXTENSION and specify the paths:
include_dirs=/usr/local/opt/sqlite/include
library_dirs=/usr/local/opt/sqlite/lib
activated the virtualenv where I want it installed, then
python setup.py build
python setup.py install
(build_static still fails with clang: error: no such file or directory: 'sqlite3.c')
(maybe I should have done pip install . as suggested in the github issue)
now the spatialite geodjango.db "SELECT InitSpatialMetaData();" succeeds, albeit with an ignorable error:
InitSpatiaMetaData() error:"table spatial_ref_sys already exists"
i.e. it's probably not even necessary to run that command
When I was istalling this i follow this instructions https://docs.djangoproject.com/en/dev/ref/contrib/gis/install/spatialite/#pysqlite2
pysqlite2
If you’ve decided to use a newer version of pysqlite2 instead of the sqlite3 Python stdlib module, then you need to make sure it can load external extensions (i.e. the required enable_load_extension method is available so SpatiaLite can be loaded).
This might involve building it yourself. For this, download pysqlite2 2.6, and untar:
$ wget https://pypi.python.org/packages/source/p/pysqlite/pysqlite-2.6.3.tar.gz
$ tar xzf pysqlite-2.6.3.tar.gz
$ cd pysqlite-2.6.3
Next, use a text editor (e.g., emacs or vi) to edit the setup.cfg file to look like the following:
[build_ext]
#define=
include_dirs=/usr/local/include
library_dirs=/usr/local/lib
libraries=sqlite3
#define=SQLITE_OMIT_LOAD_EXTENSION
I had the same error: SQLite header and source version mismatch.
For me it was enough to update libsqlite3-dev.
After that invoking $ spatialite geo.db "SELECT InitSpatialMetaData();" creates proper database.