I am trying to install pymol in CentOS 7 system. I installed the dependency glm-devel-0.9.6.3-1.el7.noarch by yum:
sudo yum install glm-devel.
During compiling I got an error related to glm as following:
layer1/SceneView.cpp:34:61: error: no matching function for call to ‘equal(const vec3&, const vec3&, float)’
Could anyone tell why this error appears?
I will appreciate any help!
Best regards.
install pymol in CentOS 7
Build example with updated glm-devel
# yum install mmtf-cpp-devel.x86_64 glew-devel.x86_64 libpng-devel freetype-devel msgpack-devel libxml2-devel python36-qt5-devel.x86_64 freeglut-devel mesa-libGL-devel.x86_64 python3-devel
# yum install ./glm-devel-0.9.9.6-6.el7.noarch.rpm
## works with the default python3 (3.6.8) and g++ -4.8.5
Link, glm-devel-0.9.9.6-6.el7 https://drive.google.com/file/d/1BXygEWqpvlbZg867dsXuW47T67Z0V0Q8/view?usp=sharing
https://github.com/schrodinger/pymol-open-source →
https://github.com/schrodinger/pymol-open-source/blob/master/INSTALL
git clone https://github.com/schrodinger/pymol-open-source.git
cd pymol-open-source/
python3 setup.py build
# python3 setup.py install
pymol ## the pymol GUI opens OK
There is also a binary version available, with python 3.7 included : https://pymol.org/2/ →
https://pymol.org/installers/PyMOL-2.5.2_293-Linux-x86_64-py37.tar.bz2 → tar xvf PyMOL-2.5.2_293-Linux-x86_64-py37.tar.bz2
cd pymol/ && ./pymol
I have downloaded the deb file from the https://support.hdfgroup.org/ftp/HDF5/releases/HDF-JAVA/hdfview-3.1.2/bin/ link and install it via
sudo dpkg -i hdfview_3.1.2-1_amd64.deb
I didn't see any error during installation.
But hdfview didn't open.
I am using java-1.11.0-openjdk and hdf5-1.10.
How to solve this problem?
I found a way to solve this. The program gets installed in /opt/hdfview. However, starting it causes the error
$ ./bin/HDFView
Error: dl failure on line 534
Error: failed /opt/hdfview/lib/runtime/lib/server/libjvm.so, because /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.32' not found (required by /opt/hdfview/lib/runtime/lib/server/libjvm.so)
Failed to launch JVM
We can fix this by patching the libjvm.so file:
Install java-15 if it is not present already:
sudo apt install openjdk-15-jre
Find the libjvm.so file:
cd /usr/lib
find . -name libjvm.so
In my case, the correct version is located in /usr/lib/jvm/java-15-openjdk-amd64/lib/server/libjvm.so
Replace the libjvm.so in hdfview with a symlink to this libjvm.so
cd /opt/hdfview/lib/runtime/lib/server
sudo mv libjvm.so libjvm.so.bak
sudo ln -s /usr/lib/jvm/java-15-openjdk-amd64/lib/server/libjvm.so libjvm.so
(optional) link the hdfview binary, so that it is found in the terminal
sudo ln -s /opt/hdfview/bin/HDFView /usr/local/bin/hdfview
Afterwards, you should be able to start hdfview both from the terminal and the icon.
I'm trying to get Docker installed on a machine with Debian 8 (Jessie), but I always seem to run into errors no matter what I try.
Using these instructions: https://docs.docker.com/install/linux/docker-ce/debian
Checking the kernal:
uname -r
3.16.0-4-686-pae
The fateful moment:
sudo apt-get install docker-ce
Setting up docker-ce (18.06.1~ce~3-0~debian) …
Installing new version of config file /etc/bash_completion.d/docker …
Job for docker.service failed. See ‘systemctl status docker.service’ and ‘journalctl -xn’ for details.
invoke-rc.d: initscript docker, action “start” failed.
dpkg: error processing package docker-ce (–configure):
subprocess installed post-installation script returned error exit status 1
Processing triggers for libc-bin (2.19-18+deb8u10) …
Errors were encountered while processing:
docker-ce
E: Sub-process /usr/bin/dpkg returned an error code (1)
I also tried installing directly from a package: https://download.docker.com/linux/debian/dists/jessie/pool/stable/amd64/
(Selecting version 17.03.2)
And after installing the dependencies, things still don't work:
sudo dpkg --install docker-ce_17.03.2_ce-0_debian-jessie_amd64.deb
(Reading database ... 169325 files and directories currently installed.)
Preparing to unpack docker-ce_17.03.2_ce-0_debian-jessie_amd64.deb ...
Unpacking docker-ce (17.03.2~ce-0~debian-jessie) over (17.03.2~ce-0~debian-jessie) ...
Setting up docker-ce (17.03.2~ce-0~debian-jessie) ...
Job for docker.service failed. See 'systemctl status docker.service' and 'journalctl -xn' for details.
invoke-rc.d: initscript docker, action "start" failed.
dpkg: error processing package docker-ce (--install):
subprocess installed post-installation script returned error exit status 1
Processing triggers for man-db (2.7.0.2-5) ...
Processing triggers for systemd (215-17+deb8u7) ...
Errors were encountered while processing:
docker-ce
I also looked at this article: http://www.boynux.com/docker-jessie/
But I didn't even get past the first step:
curl https://get.docker.com | sh
Either your platform is not easily detectable or is not supported by this
installer script.
Please visit the following URL for more detailed installation instructions:
https://docs.docker.com/engine/installation/
Between every one of these attempts I did a
sudo apt-get remove docker docker-engine docker.io docker-ce
sudo apt-get update
docker-ce isn't available for i686
see OS requirements
Docker CE is supported on both x86_64 (or amd64) and armhf architectures for Jessie and Stretch.
I have just started exploring NiftyNet.I am getting the following error when I try to run the autocontext_mr_ct_model_zoo.
When I run the following command:
python net_regress.py train \ -c ~/niftynet/extensions/autocontext_mr_ct/net_autocontext.ini \
--starting_iter 0 --max_iter 500*
I get the following error message:
ValueError: Unknown keywords in config file: [error_map] -- all possible choices are ['', u'loss_border', 'output', 'image', 'weight', 'sampler', u'cuda_devices', u'num_threads', u'num_gpus', u'model_dir', u'dataset_split_file', u'name', u'activation_function', u'batch_size', u'decay', u'reg_type', u'volume_padding_size', u'window_sampling', u'queue_length', u'multimod_foreground_type', u'histogram_ref_file', u'norm_type', u'cutoff', u'foreground_type', u'normalisation', u'whitening', u'normalise_foreground_only', u'weight_initializer', u'bias_initializer', u'weight_initializer_args', u'bias_initializer_args', u'optimiser', u'sample_per_volume', u'rotation_angle', u'rotation_angle_x', u'rotation_angle_y', u'rotation_angle_z', u'scaling_percentage', u'random_flipping_axes', u'lr', u'loss_type', u'starting_iter', u'save_every_n', u'tensorboard_every_n', u'max_iter', u'max_checkpoints', u'validation_every_n', u'validation_max_iter', u'exclude_fraction_for_validation', u'exclude_fraction_for_inference', u'inference_iter', u'save_seg_dir', u'output_interp_order', u'border', u'csv_file', u'path_to_search', u'filename_contains', u'filename_not_contains', u'interp_order', u'pixdim', u'axcodes', u'spatial_window_size'].
I'm not quite sure what I've messed up here, any advice welcomed.
Looks like the source code you downloaded is out-of-date, are you running the command with the latest version of NiftyNet?
The pip package is slightly out-of-date at the moment,
you could have the latest source code by running
git clone https://github.com/NifTK/NiftyNet.git
# installing dependencies from the list of requirements
cd NiftyNet/
pip install -r requirements-gpu.txt
# run command from the source code folder
python net_regress.py train \
-c ~/niftynet/extensions/autocontext_mr_ct/net_autocontext.ini \
--starting_iter 0 --max_iter 500
I have been working on OpenCV installation from the last 4 days but still can't find a way to install it without errors.
collect2: error: ld returned 1 exit status
apps/visualisation/CMakeFiles/opencv_visualisation.dir/build.make:104: recipe for target 'bin/opencv_visualisation' failed
make[2]: *** [bin/opencv_visualisation] Error 1
CMakeFiles/Makefile2:7461: recipe for target 'apps/visualisation/CMakeFiles/opencv_visualisation.dir/all' failed
make[1]: *** [apps/visualisation/CMakeFiles/opencv_visualisation.dir/all] Error 2
Makefile:149: recipe for target 'all' failed
make: *** [all] Error 2
It shouldn't be too difficult:
# Get all the up-to-date tools you'll need
sudo apt-get update
sudo apt-get install git cmake build-essential
# Get latest greatest OpenCV from GitHub
cd
git clone https://github.com/opencv/opencv.git
# Go build and install that puppy
cd opencv
mkdir build
cd build
cmake ..
make -j 8
sudo make install
Maybe try running the file from this link. The good thing about this is that it abstracts so many things from you. You need not manually run all the commands. Run it on the ubuntu terminal as bash install-opencv.sh.
Just let me know incase of any errors.