Quick and dirty installation¶
In this section you will have short instructions to make a typical installation of rDock.
To get the full documentation of all rDock software package and methods, please go to the Reference guide.
Moreover, you can also check the following information:
Getting started: installation and validation instructions for first-time users.
Validation experiments: instructions and examples for re-running the validation sets we have carried out.
Calculating ROC curves: tutorial for generating ROC curves and other statistics after running rDock docking jobs.
Installation in 3 steps¶
We have been able to compile rDock in the following Linux systems:
CentOS 5.5 64 bits
openSUSE 11.3 32 and 64 bits
openSUSE 12.3 32 and 64 bits
openSUSE 13.1 32 and 64 bits
Ubuntu 12.04 32 and 64 bits
Step 1¶
First of all, you will need to install several packages before compiling and running rDock:
gcc and g++ compilers version > 3.3
make
cppunit and cppunit-devel
Note
For Ubuntu users:
If you are trying to use rDock in Ubuntu, please note that csh shell is not
included in a default installation. We recommend to install csh in case some
error arises (sudo apt-get install csh), even with all the above-stated
dependencies installed.
Afterwards, download the source code compressed file or get it by SVN in Downloads section.
Step 2¶
Then, run the following commands:
$ tar -xvzf rxdock-0.1.0.tar.gz
$ cd rxdock-0.1.0/build/
and, for 32 bits computers:
$ make linux-g++
for 64 bits computers:
$ make linux-g++-64
Step 3¶
After compiling successfully, type the following command to make a test and check that your compiled version works good and the results are correct.
$ make test
If the test has succeed, you are done, enjoy using rDock!
Otherwise, please check your dependencies and all the previous commands or go to Support Section to ask for help.
Just as a concluding remark, don’t forget to set the necessary environmental variables for running rDock in the command line (for example, in Bash shell):
$ export RBT_ROOT=/path/to/rxdock/installation/
$ export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$RBT_ROOT/lib
$ export PATH=$PATH:$RBT_ROOT/bin
Installation tutorial¶
We can say that rDock has a great set of functionalities and that it is one of the best open-source high-throughput virtual screening (HTVS) suites packed with all the functionalities aspiring computational chemists need, but the major hurdle in getting new users onboard and proving it to them is the seemingly archaic way of installing and using the software. The graphical user interface is non-existent, the software itself cannot be found maintained in the relevant Linux (or macOS Homebrew, or FreeBSD Ports, etc.) repositories, you have to set up your working directory every time you start using rDock, you have to build the software from its sources, and all of that sounds very taxing and complicated to the average user, aspiring graduate students and everyone who are not tech-savvy.
Getting started to use scientific software can be daunting for anyone, especially beginners or newcomers to the field. Luckily, building and setting up rDock is much easier done than said, and we will walk you over through the entire process in this blog post. This blog post is intended for absolute beginners in Linux, scientific software in general and computational chemistry.
In this tutorial, we will be using Ubuntu 20.04 LTS as an example, but newer Ubuntu versions should work just as well.
Installing and setting up rDock¶
The good thing about command-line interface (CLI) software is that everything can be easily replicated and everyone has the same user experience. Here, you will be able to follow the guide simply by copy-pasting the commands in your terminal that comes with every Ubuntu desktop installation. Just open it up and follow the instruction further in the blog post.
Before we start, let’s convince ourselves that we’re running Ubuntu 20.04:
$ cat /etc/os-release
NAME="Ubuntu"
VERSION="20.04.3 LTS (Focal Fossa)"
ID=ubuntu
ID_LIKE=debian
PRETTY_NAME="Ubuntu 20.04.3 LTS"
VERSION_ID="20.04"
HOME_URL="https://www.ubuntu.com/"
SUPPORT_URL="https://help.ubuntu.com/"
BUG_REPORT_URL="https://bugs.launchpad.net/ubuntu/"
PRIVACY_POLICY_URL="https://www.ubuntu.com/legal/terms-and-policies/privacy-policy"
VERSION_CODENAME=focal
UBUNTU_CODENAME=focal
Alternatively, if you have neofetch installed, you can use it instead:
$ neofetch
.-/+oossssoo+/-. pnikolic@rxtxboss
`:+ssssssssssssssssss+:` -----------------
-+ssssssssssssssssssyyssss+- OS: Ubuntu 20.04.3 LTS x86_64
.ossssssssssssssssssdMMMNysssso. Host: KVM/QEMU (Standard PC (Q35 + ICH9, 2009) pc-q35-6.
/ssssssssssshdmmNNmmyNMMMMhssssss/ Kernel: 5.4.0-96-generic
+ssssssssshmydMMMMMMMNddddyssssssss+ Uptime: 55 mins
/sssssssshNMMMyhhyyyyhmNMMMNhssssssss/ Packages: 681 (dpkg), 5 (snap)
.ssssssssdMMMNhsssssssssshNMMMdssssssss. Shell: bash 5.0.17
+sssshhhyNMMNyssssssssssssyNMMMysssssss+ Resolution: 1024x768
ossyNMMMNyMMhsssssssssssssshmmmhssssssso Terminal: /dev/pts/0
ossyNMMMNyMMhsssssssssssssshmmmhssssssso CPU: AMD EPYC (with IBPB) (2) @ 3.393GHz
+sssshhhyNMMNyssssssssssssyNMMMysssssss+ GPU: 00:01.0 Red Hat, Inc. QXL paravirtual graphic card
.ssssssssdMMMNhsssssssssshNMMMdssssssss. Memory: 161MiB / 3931MiB
/sssssssshNMMMyhhyyyyhdNMMMNhssssssss/
+sssssssssdmydMMMMMMMMddddyssssssss+
/ssssssssssshdmNNNNmyNMMMMhssssss/
.ossssssssssssssssssdMMMNysssso.
-+sssssssssssssssssyyyssss+-
`:+ssssssssssssssssss+:`
.-/+oossssoo+/-.
The first thing we have to take care of is updates (in case the system isn’t
already fully up-to-date). This is done with apt update and apt upgrade
commands:
$ sudo apt update
[sudo] password for pnikolic:
Hit:1 http://hr.archive.ubuntu.com/ubuntu focal InRelease
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Hit:3 http://hr.archive.ubuntu.com/ubuntu focal-backports InRelease
Hit:4 http://hr.archive.ubuntu.com/ubuntu focal-security InRelease
Reading package lists... Done
Building dependency tree
Reading state information... Done
37 packages can be upgraded. Run 'apt list --upgradable' to see them.
$ sudo apt upgrade
Reading package lists... Done
Building dependency tree
Reading state information... Done
Calculating upgrade... Done
The following packages will be upgraded:
alsa-ucm-conf cloud-init cloud-initramfs-copymods cloud-initramfs-dyn-netconf command-not-found
libasound2 libasound2-data libdrm-common libdrm2 libnetplan0 libpam-modules libpam-modules-bin
libpam-runtime libpam0g libprocps8 libssl1.1 libudisks2-0 linux-base netplan.io open-vm-tools
openssl overlayroot procps python-apt-common python3-apt python3-commandnotfound
python3-software-properties python3-update-manager rsync snapd software-properties-common
ubuntu-advantage-tools udisks2 ufw update-manager-core update-notifier-common wget
37 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
Need to get 37.2 MB of archives.
After this operation, 1,161 kB of additional disk space will be used.
Do you want to continue? [Y/n] y
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Fetched 37.2 MB in 7s (5,471 kB/s)
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update-initramfs: Generating /boot/initrd.img-5.4.0-96-generic
Let’s continue with installing tools for obtaining and building rDock,
specifically Git, Meson,
and GNU C++ compiler. Additionally, CMake
and pkg-config are
used for finding dependencies on the system. The installation is done using the
apt install command:
$ sudo apt install git meson build-essential cmake pkg-config
Reading package lists... Done
Building dependency tree
Reading state information... Done
git is already the newest version (1:2.25.1-1ubuntu3.2).
git set to manually installed.
The following additional packages will be installed:
binutils binutils-common binutils-x86-64-linux-gnu cmake-data cpp cpp-9 dpkg-dev fakeroot g++
g++-9 gcc gcc-9 gcc-9-base libalgorithm-diff-perl libalgorithm-diff-xs-perl
libalgorithm-merge-perl libasan5 libatomic1 libbinutils libc-dev-bin libc6-dev libcc1-0
libcrypt-dev libctf-nobfd0 libctf0 libdpkg-perl libfakeroot libfile-fcntllock-perl libgcc-9-dev
libgomp1 libisl22 libitm1 libjsoncpp1 liblsan0 libmpc3 libquadmath0 librhash0 libstdc++-9-dev
libtsan0 libubsan1 linux-libc-dev make manpages-dev ninja-build
Suggested packages:
binutils-doc cmake-doc cpp-doc gcc-9-locales debian-keyring g++-multilib g++-9-multilib gcc-9-doc
gcc-multilib autoconf automake libtool flex bison gdb gcc-doc gcc-9-multilib glibc-doc bzr
libstdc++-9-doc make-doc
The following NEW packages will be installed:
binutils binutils-common binutils-x86-64-linux-gnu build-essential cmake cmake-data cpp cpp-9
dpkg-dev fakeroot g++ g++-9 gcc gcc-9 gcc-9-base libalgorithm-diff-perl libalgorithm-diff-xs-perl
libalgorithm-merge-perl libasan5 libatomic1 libbinutils libc-dev-bin libc6-dev libcc1-0
libcrypt-dev libctf-nobfd0 libctf0 libdpkg-perl libfakeroot libfile-fcntllock-perl libgcc-9-dev
libgomp1 libisl22 libitm1 libjsoncpp1 liblsan0 libmpc3 libquadmath0 librhash0 libstdc++-9-dev
libtsan0 libubsan1 linux-libc-dev make manpages-dev meson ninja-build pkg-config
0 upgraded, 48 newly installed, 0 to remove and 0 not upgraded.
Need to get 49.0 MB of archives.
After this operation, 220 MB of additional disk space will be used.
Do you want to continue? [Y/n] y
Get:1 http://hr.archive.ubuntu.com/ubuntu focal-updates/main amd64 binutils-common amd64 2.34-6ubuntu1.3 [207 kB]
Get:2 http://hr.archive.ubuntu.com/ubuntu focal-updates/main amd64 libbinutils amd64 2.34-6ubuntu1.3 [474 kB]
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Get:38 http://hr.archive.ubuntu.com/ubuntu focal/main amd64 cmake amd64 3.16.3-1ubuntu1 [3,669 kB]
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Get:41 http://hr.archive.ubuntu.com/ubuntu focal/main amd64 libalgorithm-diff-perl all 1.19.03-2 [46.6 kB]
Get:42 http://hr.archive.ubuntu.com/ubuntu focal/main amd64 libalgorithm-diff-xs-perl amd64 0.04-6 [11.3 kB]
Get:43 http://hr.archive.ubuntu.com/ubuntu focal/main amd64 libalgorithm-merge-perl all 0.08-3 [12.0 kB]
Get:44 http://hr.archive.ubuntu.com/ubuntu focal/main amd64 libfile-fcntllock-perl amd64 0.22-3build4 [33.1 kB]
Get:45 http://hr.archive.ubuntu.com/ubuntu focal/main amd64 manpages-dev all 5.05-1 [2,266 kB]
Get:46 http://hr.archive.ubuntu.com/ubuntu focal/universe amd64 ninja-build amd64 1.10.0-1build1 [107 kB]
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Of course, if you already have installed the packages before, apt will tell you.
Let’s continue by installing the required libraries, namely
Eigen, PCG,
{fmt}, and Google Test
using apt install:
$ sudo apt install libfmt-dev libeigen3-dev libpcg-cpp-dev googletest
Reading package lists... Done
Building dependency tree
Reading state information... Done
Suggested packages:
libeigen3-doc libmpfrc++-dev libfmt-doc
The following NEW packages will be installed:
googletest libeigen3-dev libfmt-dev libpcg-cpp-dev
0 upgraded, 4 newly installed, 0 to remove and 0 not upgraded.
Need to get 1,617 kB of archives.
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Get:1 http://hr.archive.ubuntu.com/ubuntu focal/universe amd64 googletest all 1.10.0-2 [623 kB]
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Setting up libfmt-dev (6.1.2+ds-2) ...
Setting up libpcg-cpp-dev (0.98.1-2) ...
If your output looks like this, you’re all set to begin installing rDock. The latest version of rDock can be found on Bitbucket, GitHub, and GitLab. The last one is the official repository and the other two are just mirroring it. We’ll be using GitLab in the following steps.
$ git clone https://gitlab.com/rxdock/rxdock.git
Cloning into 'rxdock'...
remote: Enumerating objects: 6181, done.
remote: Counting objects: 100% (2505/2505), done.
remote: Compressing objects: 100% (922/922), done.
remote: Total 6181 (delta 1874), reused 2014 (delta 1564), pack-reused 3676
Receiving objects: 100% (6181/6181), 33.53 MiB | 5.45 MiB/s, done.
Resolving deltas: 100% (4610/4610), done.
You should have the directory called rxdock with all the necessary files
downloaded from GitLab. Let’s enter that directory:
$ cd rxdock
Here we will check out the patched-rdock tag which will give us what the name says, a patched rDock. This is a good choice since documentation is still written for rDock and does not cover the latest changes in the command-line interface and configuration files.
Note
You can choose to use the latest code (in the master branch) instead of the patched-rdock tag, but be aware that there are no guarantees about its correctness or performance: in other words, it might crash and/or produce incorrect results.
$ git checkout patched-rdock
Note: switching to 'patched-rdock'.
You are in 'detached HEAD' state. You can look around, make experimental
changes and commit them, and you can discard any commits you make in this
state without impacting any branches by switching back to a branch.
If you want to create a new branch to retain commits you create, you may
do so (now or later) by using -c with the switch command. Example:
git switch -c <new-branch-name>
Or undo this operation with:
git switch -
Turn off this advice by setting config variable advice.detachedHead to false
HEAD is now at c0c3a3a Fixed MSVC error C3016
rDock’s build configuration is done
using the Meson build system. Here we set the build type
to release and enable the building of tests, which will be used to verify the
correctness of the resulting build.
$ meson -Dbuildtype=release -Dtests=true builddir
The Meson build system
Version: 0.53.2
Source dir: /home/pnikolic/rxdock
Build dir: /home/pnikolic/rxdock/builddir
Build type: native build
Project name: RxDock
Project version: 0.1.0
C++ compiler for the host machine: c++ (gcc 9.3.0 "c++ (Ubuntu 9.3.0-17ubuntu1~20.04) 9.3.0")
C++ linker for the host machine: c++ ld.bfd 2.34
Host machine cpu family: x86_64
Host machine cpu: x86_64
Found pkg-config: /usr/bin/pkg-config (0.29.1)
Run-time dependency eigen3 found: YES 3.3.7
Run-time dependency OpenMP found: YES 4.5
Found CMake: /usr/bin/cmake (3.16.3)
Run-time dependency pcg-cpp found: NO (tried pkgconfig and cmake)
Looking for a fallback subproject for the dependency pcg-cpp
Downloading pcg source from https://github.com/imneme/pcg-cpp/archive/v0.98.1.tar.gz
Downloading file of unknown size.
Downloading pcg patch from https://wrapdb.mesonbuild.com/v1/projects/pcg/0.98.1/1/get_zip
Download size: 268
Downloading: ..........
|Executing subproject pcg method meson
|
|Project name: pcg-cpp
|Project version: 0.98.1
|C++ compiler for the host machine: c++ (gcc 9.3.0 "c++ (Ubuntu 9.3.0-17ubuntu1~20.04) 9.3.0")
|C++ linker for the host machine: c++ ld.bfd 2.34
|Build targets in project: 0
|Subproject pcg finished.
Dependency pcg-cpp from subproject subprojects/pcg found: YES 0.98.1
Run-time dependency cxxopts found: NO (tried pkgconfig and cmake)
Looking for a fallback subproject for the dependency cxxopts
Downloading cxxopts source from https://github.com/jarro2783/cxxopts/archive/v2.2.0.tar.gz
Downloading file of unknown size.
Downloading cxxopts patch from https://wrapdb.mesonbuild.com/v1/projects/cxxopts/2.2.0/1/get_zip
Download size: 1022
Downloading: ..........
|Executing subproject cxxopts method meson
|
|Project name: cxxopts
|Project version: 2.2.0
|C++ compiler for the host machine: c++ (gcc 9.3.0 "c++ (Ubuntu 9.3.0-17ubuntu1~20.04) 9.3.0")
|C++ linker for the host machine: c++ ld.bfd 2.34
|Build targets in project: 1
|Subproject cxxopts finished.
Dependency cxxopts from subproject subprojects/cxxopts found: YES 2.2.0
Run-time dependency dt_smarts found: NO (tried pkgconfig and cmake)
Run-time dependency dt_smiles found: NO (tried pkgconfig and cmake)
Run-time dependency GTest found: YES (building self)
Build targets in project: 9
RxDock 0.1.0
Subprojects
cxxopts: YES
pcg: YES
Found ninja-1.10.0 at /usr/bin/ninja
Should Meson fail to find any of the dependencies listed above, use the
apt search command to find the desired package and install it manually using
apt install command. Also, should you fail to find the packages and get
stuck on this step, please use the
issue tracker to check if a
similar issue to one that you have has already been reported and report it if
it has not.
Build rDock using the ninja command:
$ ninja -C builddir
ninja: Entering directory `builddir'
[9/154] Compiling C++ object 'rxdock@sha/src_GP_RbtGPParser.cxx.o'.
../src/GP/RbtGPParser.cxx: In member function 'RbtReturnType RbtGPParser::Parse1Output(RbtGPChromosomePtr, int)':
../src/GP/RbtGPParser.cxx:78:17: warning: unused variable 'f2' [-Wunused-variable]
78 | RbtReturnType f2 = commands[ncomm]->Execute();
| ^~
[31/154] Compiling C++ object 'rxdock@sha/src_lib_RbtBond.cxx.o'.
../src/lib/RbtBond.cxx: In constructor 'RbtBond::RbtBond(int, RbtAtomPtr&, RbtAtomPtr&, int)':
../src/lib/RbtBond.cxx:33:8: warning: unused variable 'bOK1' [-Wunused-variable]
33 | bool bOK1 = m_spAtom1->AddBond(this);
| ^~~~
../src/lib/RbtBond.cxx:34:8: warning: unused variable 'bOK2' [-Wunused-variable]
34 | bool bOK2 = m_spAtom2->AddBond(this);
| ^~~~
../src/lib/RbtBond.cxx: In destructor 'virtual RbtBond::~RbtBond()':
../src/lib/RbtBond.cxx:50:8: warning: unused variable 'bOK1' [-Wunused-variable]
50 | bool bOK1 = m_spAtom1->RemoveBond(this);
| ^~~~
../src/lib/RbtBond.cxx:51:8: warning: unused variable 'bOK2' [-Wunused-variable]
51 | bool bOK2 = m_spAtom2->RemoveBond(this);
| ^~~~
[60/154] Compiling C++ object 'rxdock@sha/src_lib_RbtDockingSite.cxx.o'.
../src/lib/RbtDockingSite.cxx: In member function 'void RbtDockingSite::CreateGrid()':
../src/lib/RbtDockingSite.cxx:300:21: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
300 | for (int i = 0; i < m_spGrid->GetN(); i++) {
| ~~^~~~~~~~~~~~~~~~~~
[106/154] Compiling C++ object 'rxdock@sha/src_lib_RbtRealGrid.cxx.o'.
In file included from /usr/include/eigen3/unsupported/Eigen/CXX11/Tensor:107,
from ../include/RbtRealGrid.h:24,
from ../src/lib/RbtRealGrid.cxx:18:
/usr/include/eigen3/unsupported/Eigen/CXX11/src/Tensor/TensorEvaluator.h: In instantiation of 'struct Eigen::TensorEvaluator<const Eigen::Tensor<float, 3, 1>, Eigen::DefaultDevice>':
/usr/include/eigen3/unsupported/Eigen/CXX11/src/Tensor/TensorEvaluator.h:366:65: recursively required from 'struct Eigen::TensorEvaluator<const Eigen::TensorCwiseBinaryOp<Eigen::internal::scalar_cmp_op<float, float, Eigen::internal::cmp_GE>, const Eigen::Tensor<float, 3, 1>, const Eigen::TensorCwiseNullaryOp<Eigen::internal::scalar_constant_op<float>, const Eigen::Tensor<float, 3, 1> > >, Eigen::DefaultDevice>'
/usr/include/eigen3/unsupported/Eigen/CXX11/src/Tensor/TensorEvaluator.h:366:65: required from 'struct Eigen::TensorEvaluator<const Eigen::TensorCwiseBinaryOp<Eigen::internal::scalar_boolean_and_op, const Eigen::TensorCwiseBinaryOp<Eigen::internal::scalar_cmp_op<float, float, Eigen::internal::cmp_GE>, const Eigen::Tensor<float, 3, 1>, const Eigen::TensorCwiseNullaryOp<Eigen::internal::scalar_constant_op<float>, const Eigen::Tensor<float, 3, 1> > >, const Eigen::TensorCwiseBinaryOp<Eigen::internal::scalar_cmp_op<float, float, Eigen::internal::cmp_LT>, const Eigen::Tensor<float, 3, 1>, const Eigen::TensorCwiseNullaryOp<Eigen::internal::scalar_constant_op<float>, const Eigen::Tensor<float, 3, 1> > > >, Eigen::DefaultDevice>'
/usr/include/eigen3/unsupported/Eigen/CXX11/src/Tensor/TensorAssign.h:96:70: required from 'struct Eigen::TensorEvaluator<const Eigen::TensorAssignOp<Eigen::Tensor<bool, 3, 1>, const Eigen::TensorCwiseBinaryOp<Eigen::internal::scalar_boolean_and_op, const Eigen::TensorCwiseBinaryOp<Eigen::internal::scalar_cmp_op<float, float, Eigen::internal::cmp_GE>, const Eigen::Tensor<float, 3, 1>, const Eigen::TensorCwiseNullaryOp<Eigen::internal::scalar_constant_op<float>, const Eigen::Tensor<float, 3, 1> > >, const Eigen::TensorCwiseBinaryOp<Eigen::internal::scalar_cmp_op<float, float, Eigen::internal::cmp_LT>, const Eigen::Tensor<float, 3, 1>, const Eigen::TensorCwiseNullaryOp<Eigen::internal::scalar_constant_op<float>, const Eigen::Tensor<float, 3, 1> > > > >, Eigen::DefaultDevice>'
/usr/include/eigen3/unsupported/Eigen/CXX11/src/Tensor/Tensor.h:388:14: required from 'Eigen::Tensor<Scalar_, NumIndices_, Options_, IndexType>::Tensor(const Eigen::TensorBase<OtherDerived, 0>&) [with OtherDerived = Eigen::TensorCwiseBinaryOp<Eigen::internal::scalar_boolean_and_op, const Eigen::TensorCwiseBinaryOp<Eigen::internal::scalar_cmp_op<float, float, Eigen::internal::cmp_GE>, const Eigen::Tensor<float, 3, 1>, const Eigen::TensorCwiseNullaryOp<Eigen::internal::scalar_constant_op<float>, const Eigen::Tensor<float, 3, 1> > >, const Eigen::TensorCwiseBinaryOp<Eigen::internal::scalar_cmp_op<float, float, Eigen::internal::cmp_LT>, const Eigen::Tensor<float, 3, 1>, const Eigen::TensorCwiseNullaryOp<Eigen::internal::scalar_constant_op<float>, const Eigen::Tensor<float, 3, 1> > > >; Scalar_ = bool; int NumIndices_ = 3; int Options_ = 1; IndexType_ = long int]'
../src/lib/RbtRealGrid.cxx:207:41: required from here
/usr/include/eigen3/unsupported/Eigen/CXX11/src/Tensor/TensorEvaluator.h:162:71: warning: ignoring attributes on template argument 'Eigen::PacketType<float, Eigen::DefaultDevice>::type' {aka '__vector(4) float'} [-Wignored-attributes]
162 | PacketAccess = (internal::unpacket_traits<PacketReturnType>::size > 1),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~
In file included from /usr/include/eigen3/unsupported/Eigen/CXX11/Tensor:107,
from ../include/RbtRealGrid.h:24,
from ../src/lib/RbtRealGrid.cxx:18:
/usr/include/eigen3/unsupported/Eigen/CXX11/src/Tensor/TensorEvaluator.h: In instantiation of 'struct Eigen::TensorEvaluator<Eigen::Tensor<float, 3, 1>, Eigen::DefaultDevice>':
/usr/include/eigen3/unsupported/Eigen/CXX11/src/Tensor/TensorAssign.h:100:65: required from 'struct Eigen::TensorEvaluator<const Eigen::TensorAssignOp<Eigen::Tensor<float, 3, 1>, const Eigen::TensorSelectOp<const Eigen::Tensor<bool, 3, 1>, const Eigen::TensorCwiseNullaryOp<Eigen::internal::scalar_constant_op<float>, const Eigen::Tensor<float, 3, 1> >, const Eigen::Tensor<float, 3, 1> > >, Eigen::DefaultDevice>'
/usr/include/eigen3/unsupported/Eigen/CXX11/src/Tensor/Tensor.h:416:14: required from 'Eigen::Tensor<Scalar_, NumIndices_, Options_, IndexType>& Eigen::Tensor<Scalar_, NumIndices_, Options_, IndexType>::operator=(const OtherDerived&) [with OtherDerived = Eigen::TensorSelectOp<const Eigen::Tensor<bool, 3, 1>, const Eigen::TensorCwiseNullaryOp<Eigen::internal::scalar_constant_op<float>, const Eigen::Tensor<float, 3, 1> >, const Eigen::Tensor<float, 3, 1> >; Scalar_ = float; int NumIndices_ = 3; int Options_ = 1; IndexType_ = long int]'
../src/lib/RbtRealGrid.cxx:208:56: required from here
/usr/include/eigen3/unsupported/Eigen/CXX11/src/Tensor/TensorEvaluator.h:42:71: warning: ignoring attributes on template argument 'Eigen::PacketType<float, Eigen::DefaultDevice>::type' {aka '__vector(4) float'} [-Wignored-attributes]
42 | PacketAccess = (internal::unpacket_traits<PacketReturnType>::size > 1),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~
/usr/include/eigen3/unsupported/Eigen/CXX11/src/Tensor/TensorEvaluator.h: In instantiation of 'struct Eigen::TensorEvaluator<Eigen::Tensor<float, 0, 1>, Eigen::DefaultDevice>':
/usr/include/eigen3/unsupported/Eigen/CXX11/src/Tensor/TensorAssign.h:100:65: required from 'struct Eigen::TensorEvaluator<const Eigen::TensorAssignOp<Eigen::Tensor<float, 0, 1>, const Eigen::TensorReductionOp<Eigen::internal::MinReducer<float>, const Eigen::DimensionList<long int, 3>, const Eigen::Tensor<float, 3, 1>, Eigen::MakePointer> >, Eigen::DefaultDevice>'
/usr/include/eigen3/unsupported/Eigen/CXX11/src/Tensor/Tensor.h:388:14: required from 'Eigen::Tensor<Scalar_, NumIndices_, Options_, IndexType>::Tensor(const Eigen::TensorBase<OtherDerived, 0>&) [with OtherDerived = Eigen::TensorReductionOp<Eigen::internal::MinReducer<float>, const Eigen::DimensionList<long int, 3>, const Eigen::Tensor<float, 3, 1>, Eigen::MakePointer>; Scalar_ = float; int NumIndices_ = 0; int Options_ = 1; IndexType_ = long int]'
../src/lib/RbtRealGrid.cxx:352:70: required from here
/usr/include/eigen3/unsupported/Eigen/CXX11/src/Tensor/TensorEvaluator.h:42:71: warning: ignoring attributes on template argument 'Eigen::PacketType<float, Eigen::DefaultDevice>::type' {aka '__vector(4) float'} [-Wignored-attributes]
In file included from /usr/include/eigen3/unsupported/Eigen/CXX11/Tensor:141,
from ../include/RbtRealGrid.h:24,
from ../src/lib/RbtRealGrid.cxx:18:
/usr/include/eigen3/unsupported/Eigen/CXX11/src/Tensor/TensorExecutor.h: In instantiation of 'static void Eigen::internal::TensorExecutor<Expression, Eigen::DefaultDevice, true>::run(const Expression&, const Eigen::DefaultDevice&) [with Expression = const Eigen::TensorAssignOp<Eigen::Tensor<float, 3, 1>, const Eigen::TensorSelectOp<const Eigen::Tensor<bool, 3, 1>, const Eigen::TensorCwiseNullaryOp<Eigen::internal::scalar_constant_op<float>, const Eigen::Tensor<float, 3, 1> >, const Eigen::Tensor<float, 3, 1> > >]':
/usr/include/eigen3/unsupported/Eigen/CXX11/src/Tensor/Tensor.h:417:65: required from 'Eigen::Tensor<Scalar_, NumIndices_, Options_, IndexType>& Eigen::Tensor<Scalar_, NumIndices_, Options_, IndexType>::operator=(const OtherDerived&) [with OtherDerived = Eigen::TensorSelectOp<const Eigen::Tensor<bool, 3, 1>, const Eigen::TensorCwiseNullaryOp<Eigen::internal::scalar_constant_op<float>, const Eigen::Tensor<float, 3, 1> >, const Eigen::Tensor<float, 3, 1> >; Scalar_ = float; int NumIndices_ = 3; int Options_ = 1; IndexType_ = long int]'
../src/lib/RbtRealGrid.cxx:208:56: required from here
/usr/include/eigen3/unsupported/Eigen/CXX11/src/Tensor/TensorExecutor.h:61:17: warning: ignoring attributes on template argument 'Eigen::TensorEvaluator<const Eigen::TensorAssignOp<Eigen::Tensor<float, 3, 1>, const Eigen::TensorSelectOp<const Eigen::Tensor<bool, 3, 1>, const Eigen::TensorCwiseNullaryOp<Eigen::internal::scalar_constant_op<float>, const Eigen::Tensor<float, 3, 1> >, const Eigen::Tensor<float, 3, 1> > >, Eigen::DefaultDevice>::PacketReturnType' {aka '__vector(4) float'} [-Wignored-attributes]
61 | const int PacketSize = unpacket_traits<typename TensorEvaluator<Expression, DefaultDevice>::PacketReturnType>::size;
| ^~~~~~~~~~
/usr/include/eigen3/unsupported/Eigen/CXX11/src/Tensor/TensorExecutor.h: In instantiation of 'static void Eigen::internal::TensorExecutor<Expression, Eigen::DefaultDevice, true>::run(const Expression&, const Eigen::DefaultDevice&) [with Expression = const Eigen::TensorAssignOp<Eigen::Tensor<float, 0, 1>, const Eigen::TensorReductionOp<Eigen::internal::MinReducer<float>, const Eigen::DimensionList<long int, 3>, const Eigen::Tensor<float, 3, 1>, Eigen::MakePointer> >]':
/usr/include/eigen3/unsupported/Eigen/CXX11/src/Tensor/Tensor.h:389:65: required from 'Eigen::Tensor<Scalar_, NumIndices_, Options_, IndexType>::Tensor(const Eigen::TensorBase<OtherDerived, 0>&) [with OtherDerived = Eigen::TensorReductionOp<Eigen::internal::MinReducer<float>, const Eigen::DimensionList<long int, 3>, const Eigen::Tensor<float, 3, 1>, Eigen::MakePointer>; Scalar_ = float; int NumIndices_ = 0; int Options_ = 1; IndexType_ = long int]'
../src/lib/RbtRealGrid.cxx:352:70: required from here
/usr/include/eigen3/unsupported/Eigen/CXX11/src/Tensor/TensorExecutor.h:61:17: warning: ignoring attributes on template argument 'Eigen::TensorEvaluator<const Eigen::TensorAssignOp<Eigen::Tensor<float, 0, 1>, const Eigen::TensorReductionOp<Eigen::internal::MinReducer<float>, const Eigen::DimensionList<long int, 3>, const Eigen::Tensor<float, 3, 1>, Eigen::MakePointer> >, Eigen::DefaultDevice>::PacketReturnType' {aka '__vector(4) float'} [-Wignored-attributes]
/usr/include/eigen3/unsupported/Eigen/CXX11/src/Tensor/TensorExecutor.h: In instantiation of 'static void Eigen::internal::TensorExecutor<Expression, Eigen::DefaultDevice, true>::run(const Expression&, const Eigen::DefaultDevice&) [with Expression = const Eigen::TensorAssignOp<Eigen::Tensor<float, 0, 1>, const Eigen::TensorReductionOp<Eigen::internal::MaxReducer<float>, const Eigen::DimensionList<long int, 3>, const Eigen::Tensor<float, 3, 1>, Eigen::MakePointer> >]':
/usr/include/eigen3/unsupported/Eigen/CXX11/src/Tensor/Tensor.h:389:65: required from 'Eigen::Tensor<Scalar_, NumIndices_, Options_, IndexType>::Tensor(const Eigen::TensorBase<OtherDerived, 0>&) [with OtherDerived = Eigen::TensorReductionOp<Eigen::internal::MaxReducer<float>, const Eigen::DimensionList<long int, 3>, const Eigen::Tensor<float, 3, 1>, Eigen::MakePointer>; Scalar_ = float; int NumIndices_ = 0; int Options_ = 1; IndexType_ = long int]'
../src/lib/RbtRealGrid.cxx:357:70: required from here
/usr/include/eigen3/unsupported/Eigen/CXX11/src/Tensor/TensorExecutor.h:61:17: warning: ignoring attributes on template argument 'Eigen::TensorEvaluator<const Eigen::TensorAssignOp<Eigen::Tensor<float, 0, 1>, const Eigen::TensorReductionOp<Eigen::internal::MaxReducer<float>, const Eigen::DimensionList<long int, 3>, const Eigen::Tensor<float, 3, 1>, Eigen::MakePointer> >, Eigen::DefaultDevice>::PacketReturnType' {aka '__vector(4) float'} [-Wignored-attributes]
/usr/include/eigen3/unsupported/Eigen/CXX11/src/Tensor/TensorExecutor.h: In instantiation of 'static void Eigen::internal::TensorExecutor<Expression, Eigen::DefaultDevice, true>::run(const Expression&, const Eigen::DefaultDevice&) [with Expression = const Eigen::TensorAssignOp<Eigen::Tensor<float, 3, 1>, const Eigen::Tensor<float, 3, 1> >]':
/usr/include/eigen3/unsupported/Eigen/CXX11/src/Tensor/Tensor.h:407:65: required from 'Eigen::Tensor<Scalar_, NumIndices_, Options_, IndexType>& Eigen::Tensor<Scalar_, NumIndices_, Options_, IndexType>::operator=(const Eigen::Tensor<Scalar_, NumIndices_, Options_, IndexType>&) [with Scalar_ = float; int NumIndices_ = 3; int Options_ = 1; IndexType_ = long int]'
../src/lib/RbtRealGrid.cxx:520:63: required from here
/usr/include/eigen3/unsupported/Eigen/CXX11/src/Tensor/TensorExecutor.h:61:17: warning: ignoring attributes on template argument 'Eigen::TensorEvaluator<const Eigen::TensorAssignOp<Eigen::Tensor<float, 3, 1>, const Eigen::Tensor<float, 3, 1> >, Eigen::DefaultDevice>::PacketReturnType' {aka '__vector(4) float'} [-Wignored-attributes]
/usr/include/eigen3/unsupported/Eigen/CXX11/src/Tensor/TensorExecutor.h: In instantiation of 'static void Eigen::internal::TensorExecutor<Expression, Eigen::DefaultDevice, true>::run(const Expression&, const Eigen::DefaultDevice&) [with Expression = const Eigen::TensorAssignOp<Eigen::Tensor<float, 3, 1>, const Eigen::TensorCwiseNullaryOp<Eigen::internal::scalar_constant_op<float>, const Eigen::Tensor<float, 3, 1> > >]':
/usr/include/eigen3/unsupported/Eigen/CXX11/src/Tensor/Tensor.h:417:65: required from 'Eigen::Tensor<Scalar_, NumIndices_, Options_, IndexType>& Eigen::Tensor<Scalar_, NumIndices_, Options_, IndexType>::operator=(const OtherDerived&) [with OtherDerived = Eigen::TensorCwiseNullaryOp<Eigen::internal::scalar_constant_op<float>, const Eigen::Tensor<float, 3, 1> >; Scalar_ = float; int NumIndices_ = 3; int Options_ = 1; IndexType_ = long int]'
/usr/include/eigen3/unsupported/Eigen/CXX11/src/Tensor/TensorBase.h:847:24: required from 'Derived& Eigen::TensorBase<Derived, AccessLevel>::setConstant(const Scalar&) [with Derived = Eigen::Tensor<float, 3, 1>; int AccessLevel = 1; Eigen::TensorBase<Derived, AccessLevel>::Scalar = float]'
../src/lib/RbtRealGrid.cxx:200:68: required from here
/usr/include/eigen3/unsupported/Eigen/CXX11/src/Tensor/TensorExecutor.h:61:17: warning: ignoring attributes on template argument 'Eigen::TensorEvaluator<const Eigen::TensorAssignOp<Eigen::Tensor<float, 3, 1>, const Eigen::TensorCwiseNullaryOp<Eigen::internal::scalar_constant_op<float>, const Eigen::Tensor<float, 3, 1> > >, Eigen::DefaultDevice>::PacketReturnType' {aka '__vector(4) float'} [-Wignored-attributes]
In file included from /usr/include/eigen3/unsupported/Eigen/CXX11/Tensor:107,
from ../include/RbtRealGrid.h:24,
from ../src/lib/RbtRealGrid.cxx:18:
/usr/include/eigen3/unsupported/Eigen/CXX11/src/Tensor/TensorEvaluator.h: In instantiation of 'const int Eigen::TensorEvaluator<const Eigen::TensorSelectOp<const Eigen::Tensor<bool, 3, 1>, const Eigen::TensorCwiseNullaryOp<Eigen::internal::scalar_constant_op<float>, const Eigen::Tensor<float, 3, 1> >, const Eigen::Tensor<float, 3, 1> >, Eigen::DefaultDevice>::PacketSize':
/usr/include/eigen3/unsupported/Eigen/CXX11/src/Tensor/TensorEvaluator.h:600:36: required from 'Eigen::TensorEvaluator<const Eigen::TensorSelectOp<IfArgType, ThenArgType, ElseArgType>, Device>::PacketReturnType Eigen::TensorEvaluator<const Eigen::TensorSelectOp<IfArgType, ThenArgType, ElseArgType>, Device>::packet(Eigen::TensorEvaluator<const Eigen::TensorSelectOp<IfArgType, ThenArgType, ElseArgType>, Device>::Index) const [with int LoadMode = 16; IfArgType = const Eigen::Tensor<bool, 3, 1>; ThenArgType = const Eigen::TensorCwiseNullaryOp<Eigen::internal::scalar_constant_op<float>, const Eigen::Tensor<float, 3, 1> >; ElseArgType = const Eigen::Tensor<float, 3, 1>; Device = Eigen::DefaultDevice; Eigen::TensorEvaluator<const Eigen::TensorSelectOp<IfArgType, ThenArgType, ElseArgType>, Device>::PacketReturnType = __vector(4) float; Eigen::TensorEvaluator<const Eigen::TensorSelectOp<IfArgType, ThenArgType, ElseArgType>, Device>::Index = long int]'
/usr/include/eigen3/unsupported/Eigen/CXX11/src/Tensor/TensorAssign.h:141:5: required from 'void Eigen::TensorEvaluator<const Eigen::TensorAssignOp<LhsXprType, RhsXprType>, Device>::evalPacket(Eigen::TensorEvaluator<const Eigen::TensorAssignOp<LhsXprType, RhsXprType>, Device>::Index) [with LeftArgType = Eigen::Tensor<float, 3, 1>; RightArgType = const Eigen::TensorSelectOp<const Eigen::Tensor<bool, 3, 1>, const Eigen::TensorCwiseNullaryOp<Eigen::internal::scalar_constant_op<float>, const Eigen::Tensor<float, 3, 1> >, const Eigen::Tensor<float, 3, 1> >; Device = Eigen::DefaultDevice; Eigen::TensorEvaluator<const Eigen::TensorAssignOp<LhsXprType, RhsXprType>, Device>::Index = long int]'
/usr/include/eigen3/unsupported/Eigen/CXX11/src/Tensor/TensorExecutor.h:68:11: required from 'static void Eigen::internal::TensorExecutor<Expression, Eigen::DefaultDevice, true>::run(const Expression&, const Eigen::DefaultDevice&) [with Expression = const Eigen::TensorAssignOp<Eigen::Tensor<float, 3, 1>, const Eigen::TensorSelectOp<const Eigen::Tensor<bool, 3, 1>, const Eigen::TensorCwiseNullaryOp<Eigen::internal::scalar_constant_op<float>, const Eigen::Tensor<float, 3, 1> >, const Eigen::Tensor<float, 3, 1> > >]'
/usr/include/eigen3/unsupported/Eigen/CXX11/src/Tensor/Tensor.h:417:65: required from 'Eigen::Tensor<Scalar_, NumIndices_, Options_, IndexType>& Eigen::Tensor<Scalar_, NumIndices_, Options_, IndexType>::operator=(const OtherDerived&) [with OtherDerived = Eigen::TensorSelectOp<const Eigen::Tensor<bool, 3, 1>, const Eigen::TensorCwiseNullaryOp<Eigen::internal::scalar_constant_op<float>, const Eigen::Tensor<float, 3, 1> >, const Eigen::Tensor<float, 3, 1> >; Scalar_ = float; int NumIndices_ = 3; int Options_ = 1; IndexType_ = long int]'
../src/lib/RbtRealGrid.cxx:208:56: required from here
/usr/include/eigen3/unsupported/Eigen/CXX11/src/Tensor/TensorEvaluator.h:572:20: warning: ignoring attributes on template argument 'Eigen::PacketType<float, Eigen::DefaultDevice>::type' {aka '__vector(4) float'} [-Wignored-attributes]
572 | static const int PacketSize = internal::unpacket_traits<PacketReturnType>::size;
| ^~~~~~~~~~
In file included from /usr/include/eigen3/unsupported/Eigen/CXX11/Tensor:109,
from ../include/RbtRealGrid.h:24,
from ../src/lib/RbtRealGrid.cxx:18:
/usr/include/eigen3/unsupported/Eigen/CXX11/src/Tensor/TensorReduction.h: In instantiation of 'const int Eigen::TensorEvaluator<const Eigen::TensorReductionOp<Eigen::internal::MinReducer<float>, const Eigen::DimensionList<long int, 3>, const Eigen::Tensor<float, 3, 1>, Eigen::MakePointer>, Eigen::DefaultDevice>::PacketSize':
/usr/include/eigen3/unsupported/Eigen/CXX11/src/Tensor/TensorReduction.h:613:5: required from 'Eigen::TensorEvaluator<const Eigen::TensorReductionOp<Op, Dims, XprType, MakePointer_>, Device>::PacketReturnType Eigen::TensorEvaluator<const Eigen::TensorReductionOp<Op, Dims, XprType, MakePointer_>, Device>::packet(Eigen::TensorEvaluator<const Eigen::TensorReductionOp<Op, Dims, XprType, MakePointer_>, Device>::Index) const [with int LoadMode = 0; Op = Eigen::internal::MinReducer<float>; Dims = const Eigen::DimensionList<long int, 3>; ArgType = const Eigen::Tensor<float, 3, 1>; MakePointer_ = Eigen::MakePointer; Device = Eigen::DefaultDevice; Eigen::TensorEvaluator<const Eigen::TensorReductionOp<Op, Dims, XprType, MakePointer_>, Device>::PacketReturnType = __vector(4) float; Eigen::TensorEvaluator<const Eigen::TensorReductionOp<Op, Dims, XprType, MakePointer_>, Device>::Index = long int]'
/usr/include/eigen3/unsupported/Eigen/CXX11/src/Tensor/TensorAssign.h:141:5: required from 'void Eigen::TensorEvaluator<const Eigen::TensorAssignOp<LhsXprType, RhsXprType>, Device>::evalPacket(Eigen::TensorEvaluator<const Eigen::TensorAssignOp<LhsXprType, RhsXprType>, Device>::Index) [with LeftArgType = Eigen::Tensor<float, 0, 1>; RightArgType = const Eigen::TensorReductionOp<Eigen::internal::MinReducer<float>, const Eigen::DimensionList<long int, 3>, const Eigen::Tensor<float, 3, 1>, Eigen::MakePointer>; Device = Eigen::DefaultDevice; Eigen::TensorEvaluator<const Eigen::TensorAssignOp<LhsXprType, RhsXprType>, Device>::Index = long int]'
/usr/include/eigen3/unsupported/Eigen/CXX11/src/Tensor/TensorExecutor.h:68:11: required from 'static void Eigen::internal::TensorExecutor<Expression, Eigen::DefaultDevice, true>::run(const Expression&, const Eigen::DefaultDevice&) [with Expression = const Eigen::TensorAssignOp<Eigen::Tensor<float, 0, 1>, const Eigen::TensorReductionOp<Eigen::internal::MinReducer<float>, const Eigen::DimensionList<long int, 3>, const Eigen::Tensor<float, 3, 1>, Eigen::MakePointer> >]'
/usr/include/eigen3/unsupported/Eigen/CXX11/src/Tensor/Tensor.h:389:65: required from 'Eigen::Tensor<Scalar_, NumIndices_, Options_, IndexType>::Tensor(const Eigen::TensorBase<OtherDerived, 0>&) [with OtherDerived = Eigen::TensorReductionOp<Eigen::internal::MinReducer<float>, const Eigen::DimensionList<long int, 3>, const Eigen::Tensor<float, 3, 1>, Eigen::MakePointer>; Scalar_ = float; int NumIndices_ = 0; int Options_ = 1; IndexType_ = long int]'
../src/lib/RbtRealGrid.cxx:352:70: required from here
/usr/include/eigen3/unsupported/Eigen/CXX11/src/Tensor/TensorReduction.h:397:20: warning: ignoring attributes on template argument 'Eigen::PacketType<float, Eigen::DefaultDevice>::type' {aka '__vector(4) float'} [-Wignored-attributes]
397 | static const int PacketSize = internal::unpacket_traits<PacketReturnType>::size;
| ^~~~~~~~~~
/usr/include/eigen3/unsupported/Eigen/CXX11/src/Tensor/TensorReduction.h: In instantiation of 'const int Eigen::TensorEvaluator<const Eigen::TensorReductionOp<Eigen::internal::MaxReducer<float>, const Eigen::DimensionList<long int, 3>, const Eigen::Tensor<float, 3, 1>, Eigen::MakePointer>, Eigen::DefaultDevice>::PacketSize':
/usr/include/eigen3/unsupported/Eigen/CXX11/src/Tensor/TensorReduction.h:613:5: required from 'Eigen::TensorEvaluator<const Eigen::TensorReductionOp<Op, Dims, XprType, MakePointer_>, Device>::PacketReturnType Eigen::TensorEvaluator<const Eigen::TensorReductionOp<Op, Dims, XprType, MakePointer_>, Device>::packet(Eigen::TensorEvaluator<const Eigen::TensorReductionOp<Op, Dims, XprType, MakePointer_>, Device>::Index) const [with int LoadMode = 0; Op = Eigen::internal::MaxReducer<float>; Dims = const Eigen::DimensionList<long int, 3>; ArgType = const Eigen::Tensor<float, 3, 1>; MakePointer_ = Eigen::MakePointer; Device = Eigen::DefaultDevice; Eigen::TensorEvaluator<const Eigen::TensorReductionOp<Op, Dims, XprType, MakePointer_>, Device>::PacketReturnType = __vector(4) float; Eigen::TensorEvaluator<const Eigen::TensorReductionOp<Op, Dims, XprType, MakePointer_>, Device>::Index = long int]'
/usr/include/eigen3/unsupported/Eigen/CXX11/src/Tensor/TensorAssign.h:141:5: required from 'void Eigen::TensorEvaluator<const Eigen::TensorAssignOp<LhsXprType, RhsXprType>, Device>::evalPacket(Eigen::TensorEvaluator<const Eigen::TensorAssignOp<LhsXprType, RhsXprType>, Device>::Index) [with LeftArgType = Eigen::Tensor<float, 0, 1>; RightArgType = const Eigen::TensorReductionOp<Eigen::internal::MaxReducer<float>, const Eigen::DimensionList<long int, 3>, const Eigen::Tensor<float, 3, 1>, Eigen::MakePointer>; Device = Eigen::DefaultDevice; Eigen::TensorEvaluator<const Eigen::TensorAssignOp<LhsXprType, RhsXprType>, Device>::Index = long int]'
/usr/include/eigen3/unsupported/Eigen/CXX11/src/Tensor/TensorExecutor.h:68:11: required from 'static void Eigen::internal::TensorExecutor<Expression, Eigen::DefaultDevice, true>::run(const Expression&, const Eigen::DefaultDevice&) [with Expression = const Eigen::TensorAssignOp<Eigen::Tensor<float, 0, 1>, const Eigen::TensorReductionOp<Eigen::internal::MaxReducer<float>, const Eigen::DimensionList<long int, 3>, const Eigen::Tensor<float, 3, 1>, Eigen::MakePointer> >]'
/usr/include/eigen3/unsupported/Eigen/CXX11/src/Tensor/Tensor.h:389:65: required from 'Eigen::Tensor<Scalar_, NumIndices_, Options_, IndexType>::Tensor(const Eigen::TensorBase<OtherDerived, 0>&) [with OtherDerived = Eigen::TensorReductionOp<Eigen::internal::MaxReducer<float>, const Eigen::DimensionList<long int, 3>, const Eigen::Tensor<float, 3, 1>, Eigen::MakePointer>; Scalar_ = float; int NumIndices_ = 0; int Options_ = 1; IndexType_ = long int]'
../src/lib/RbtRealGrid.cxx:357:70: required from here
/usr/include/eigen3/unsupported/Eigen/CXX11/src/Tensor/TensorReduction.h:397:20: warning: ignoring attributes on template argument 'Eigen::PacketType<float, Eigen::DefaultDevice>::type' {aka '__vector(4) float'} [-Wignored-attributes]
/usr/include/eigen3/unsupported/Eigen/CXX11/src/Tensor/TensorReduction.h: In instantiation of 'static typename Self::CoeffReturnType Eigen::internal::InnerMostDimReducer<Self, Op, true>::reduce(const Self&, typename Self::Index, typename Self::Index, Op&) [with Self = Eigen::TensorEvaluator<const Eigen::TensorReductionOp<Eigen::internal::MinReducer<float>, const Eigen::DimensionList<long int, 3>, const Eigen::Tensor<float, 3, 1>, Eigen::MakePointer>, Eigen::DefaultDevice>; Op = Eigen::internal::MinReducer<float>; typename Self::CoeffReturnType = float; typename Self::Index = long int]':
/usr/include/eigen3/unsupported/Eigen/CXX11/src/Tensor/TensorReduction.h:627:68: required from 'Eigen::TensorEvaluator<const Eigen::TensorReductionOp<Op, Dims, XprType, MakePointer_>, Device>::PacketReturnType Eigen::TensorEvaluator<const Eigen::TensorReductionOp<Op, Dims, XprType, MakePointer_>, Device>::packet(Eigen::TensorEvaluator<const Eigen::TensorReductionOp<Op, Dims, XprType, MakePointer_>, Device>::Index) const [with int LoadMode = 0; Op = Eigen::internal::MinReducer<float>; Dims = const Eigen::DimensionList<long int, 3>; ArgType = const Eigen::Tensor<float, 3, 1>; MakePointer_ = Eigen::MakePointer; Device = Eigen::DefaultDevice; Eigen::TensorEvaluator<const Eigen::TensorReductionOp<Op, Dims, XprType, MakePointer_>, Device>::PacketReturnType = __vector(4) float; Eigen::TensorEvaluator<const Eigen::TensorReductionOp<Op, Dims, XprType, MakePointer_>, Device>::Index = long int]'
/usr/include/eigen3/unsupported/Eigen/CXX11/src/Tensor/TensorAssign.h:141:5: required from 'void Eigen::TensorEvaluator<const Eigen::TensorAssignOp<LhsXprType, RhsXprType>, Device>::evalPacket(Eigen::TensorEvaluator<const Eigen::TensorAssignOp<LhsXprType, RhsXprType>, Device>::Index) [with LeftArgType = Eigen::Tensor<float, 0, 1>; RightArgType = const Eigen::TensorReductionOp<Eigen::internal::MinReducer<float>, const Eigen::DimensionList<long int, 3>, const Eigen::Tensor<float, 3, 1>, Eigen::MakePointer>; Device = Eigen::DefaultDevice; Eigen::TensorEvaluator<const Eigen::TensorAssignOp<LhsXprType, RhsXprType>, Device>::Index = long int]'
/usr/include/eigen3/unsupported/Eigen/CXX11/src/Tensor/TensorExecutor.h:68:11: required from 'static void Eigen::internal::TensorExecutor<Expression, Eigen::DefaultDevice, true>::run(const Expression&, const Eigen::DefaultDevice&) [with Expression = const Eigen::TensorAssignOp<Eigen::Tensor<float, 0, 1>, const Eigen::TensorReductionOp<Eigen::internal::MinReducer<float>, const Eigen::DimensionList<long int, 3>, const Eigen::Tensor<float, 3, 1>, Eigen::MakePointer> >]'
/usr/include/eigen3/unsupported/Eigen/CXX11/src/Tensor/Tensor.h:389:65: required from 'Eigen::Tensor<Scalar_, NumIndices_, Options_, IndexType>::Tensor(const Eigen::TensorBase<OtherDerived, 0>&) [with OtherDerived = Eigen::TensorReductionOp<Eigen::internal::MinReducer<float>, const Eigen::DimensionList<long int, 3>, const Eigen::Tensor<float, 3, 1>, Eigen::MakePointer>; Scalar_ = float; int NumIndices_ = 0; int Options_ = 1; IndexType_ = long int]'
../src/lib/RbtRealGrid.cxx:352:70: required from here
/usr/include/eigen3/unsupported/Eigen/CXX11/src/Tensor/TensorReduction.h:169:15: warning: ignoring attributes on template argument 'Eigen::TensorEvaluator<const Eigen::TensorReductionOp<Eigen::internal::MinReducer<float>, const Eigen::DimensionList<long int, 3>, const Eigen::Tensor<float, 3, 1>, Eigen::MakePointer>, Eigen::DefaultDevice>::PacketReturnType' {aka '__vector(4) float'} [-Wignored-attributes]
169 | const int packetSize = internal::unpacket_traits<typename Self::PacketReturnType>::size;
| ^~~~~~~~~~
/usr/include/eigen3/unsupported/Eigen/CXX11/src/Tensor/TensorReduction.h: In instantiation of 'static typename Self::CoeffReturnType Eigen::internal::InnerMostDimReducer<Self, Op, true>::reduce(const Self&, typename Self::Index, typename Self::Index, Op&) [with Self = Eigen::TensorEvaluator<const Eigen::TensorReductionOp<Eigen::internal::MaxReducer<float>, const Eigen::DimensionList<long int, 3>, const Eigen::Tensor<float, 3, 1>, Eigen::MakePointer>, Eigen::DefaultDevice>; Op = Eigen::internal::MaxReducer<float>; typename Self::CoeffReturnType = float; typename Self::Index = long int]':
/usr/include/eigen3/unsupported/Eigen/CXX11/src/Tensor/TensorReduction.h:627:68: required from 'Eigen::TensorEvaluator<const Eigen::TensorReductionOp<Op, Dims, XprType, MakePointer_>, Device>::PacketReturnType Eigen::TensorEvaluator<const Eigen::TensorReductionOp<Op, Dims, XprType, MakePointer_>, Device>::packet(Eigen::TensorEvaluator<const Eigen::TensorReductionOp<Op, Dims, XprType, MakePointer_>, Device>::Index) const [with int LoadMode = 0; Op = Eigen::internal::MaxReducer<float>; Dims = const Eigen::DimensionList<long int, 3>; ArgType = const Eigen::Tensor<float, 3, 1>; MakePointer_ = Eigen::MakePointer; Device = Eigen::DefaultDevice; Eigen::TensorEvaluator<const Eigen::TensorReductionOp<Op, Dims, XprType, MakePointer_>, Device>::PacketReturnType = __vector(4) float; Eigen::TensorEvaluator<const Eigen::TensorReductionOp<Op, Dims, XprType, MakePointer_>, Device>::Index = long int]'
/usr/include/eigen3/unsupported/Eigen/CXX11/src/Tensor/TensorAssign.h:141:5: required from 'void Eigen::TensorEvaluator<const Eigen::TensorAssignOp<LhsXprType, RhsXprType>, Device>::evalPacket(Eigen::TensorEvaluator<const Eigen::TensorAssignOp<LhsXprType, RhsXprType>, Device>::Index) [with LeftArgType = Eigen::Tensor<float, 0, 1>; RightArgType = const Eigen::TensorReductionOp<Eigen::internal::MaxReducer<float>, const Eigen::DimensionList<long int, 3>, const Eigen::Tensor<float, 3, 1>, Eigen::MakePointer>; Device = Eigen::DefaultDevice; Eigen::TensorEvaluator<const Eigen::TensorAssignOp<LhsXprType, RhsXprType>, Device>::Index = long int]'
/usr/include/eigen3/unsupported/Eigen/CXX11/src/Tensor/TensorExecutor.h:68:11: required from 'static void Eigen::internal::TensorExecutor<Expression, Eigen::DefaultDevice, true>::run(const Expression&, const Eigen::DefaultDevice&) [with Expression = const Eigen::TensorAssignOp<Eigen::Tensor<float, 0, 1>, const Eigen::TensorReductionOp<Eigen::internal::MaxReducer<float>, const Eigen::DimensionList<long int, 3>, const Eigen::Tensor<float, 3, 1>, Eigen::MakePointer> >]'
/usr/include/eigen3/unsupported/Eigen/CXX11/src/Tensor/Tensor.h:389:65: required from 'Eigen::Tensor<Scalar_, NumIndices_, Options_, IndexType>::Tensor(const Eigen::TensorBase<OtherDerived, 0>&) [with OtherDerived = Eigen::TensorReductionOp<Eigen::internal::MaxReducer<float>, const Eigen::DimensionList<long int, 3>, const Eigen::Tensor<float, 3, 1>, Eigen::MakePointer>; Scalar_ = float; int NumIndices_ = 0; int Options_ = 1; IndexType_ = long int]'
../src/lib/RbtRealGrid.cxx:357:70: required from here
/usr/include/eigen3/unsupported/Eigen/CXX11/src/Tensor/TensorReduction.h:169:15: warning: ignoring attributes on template argument 'Eigen::TensorEvaluator<const Eigen::TensorReductionOp<Eigen::internal::MaxReducer<float>, const Eigen::DimensionList<long int, 3>, const Eigen::Tensor<float, 3, 1>, Eigen::MakePointer>, Eigen::DefaultDevice>::PacketReturnType' {aka '__vector(4) float'} [-Wignored-attributes]
[130/154] Compiling C++ object 'rxdock@sha/src_lib_RbtVdwSF.cxx.o'.
../src/lib/RbtVdwSF.cxx: In member function 'void RbtVdwSF::Setup()':
../src/lib/RbtVdwSF.cxx:364:36: warning: 'alphai' may be used uninitialized in this function [-Wmaybe-uninitialized]
364 | double D = 0.345 * Ii * Ij * alphai * alphaj / (Ii + Ij);
| ~~~~~~~~~~~~~~~~^~~~~~~~
../src/lib/RbtVdwSF.cxx:364:60: warning: 'Ii' may be used uninitialized in this function [-Wmaybe-uninitialized]
364 | double D = 0.345 * Ii * Ij * alphai * alphaj / (Ii + Ij);
| ~~~~^~~~~
[154/154] Linking target unit-test.
Run the tests, also using the ninja command, but this time with the argument
test:
$ ninja -C builddir test
ninja: Entering directory 'builddir'
[0/1] Running all tests.
1/5 rbcavity-1koc OK 0.87 s
2/5 rbcavity-1yet OK 6.68 s
3/5 rbcavity-1yet-test OK 6.29 s
4/5 unit-test OK 11.84 s
5/5 rbdock-1yet-test OK 1.77 s
Ok: 5
Expected Fail: 0
Fail: 0
Unexpected Pass: 0
Skipped: 0
Timeout: 0
Full log written to /home/pnikolic/rxdock/builddir/meson-logs/testlog.txt
If everything went fine, your system is up to date, and you followed these instructions to the letter – congratulations! rDock is now successfully built and tested on your desktop or laptop computer, and you can start using it immediately.
To check where your rDock is built, go to your rxdock directory and run
pwd:
$ pwd
/home/pnikolic/rxdock
In order to start using rDock, we have to set up a working environment. Go back to your home directory in the current terminal or open up a new terminal.
$ cd
Make a new directory called training, and enter it.
$ mkdir training
$ cd training
Remember the path we obtained via the pwd command? Now is the time to use
it. Execute the following instructions and modify the RBT_ROOT path to
correspond to that path, in the same manner, the code below corresponds to my
path in the shown above.
$ export RBT_ROOT=/home/pnikolic/rxdock
$ export PATH=$RBT_ROOT/bin:$PATH
$ export PERL5LIB=$RBT_ROOT/lib:$PERL5LIB
$ export PATH=$RBT_ROOT/builddir:$PATH
$ export LD_LIBRARY_PATH=$RBT_ROOT/builddir:$LD_LIBRARY_PATH
Let us verify that the rDock is properly installed and the working environment
is properly set up by running rbcavity and rbdock commands with the
parameter --help or -h:
$ rbcavity -h
***********************************************
The RxDock molecular docking program is licensed under GNU LGPL version 3.
RxDock is maintained by Vedran Miletić, Patrik Nikolić, and Luka Vretenar.
Visit https://rxdock.gitlab.io/ for more information.
Executable: rbcavity/0.1.0
Library: librxdock.so/0.1.0
RBT_ROOT: /home/pnikolic/rxdock
RBT_HOME: /home/pnikolic
Current dir: /home/pnikolic/rxdock
Date: Thu Jan 27 22:02:56 2022
***********************************************
rbcavity - calculate docking cavities
Usage:
rbcavity [OPTION...]
-r, --receptor-param arg receptor param file (contains active site
params)
-W, --write-docking-cavities write docking cavities (plus distance grid)
to .as file
-R, --read-docking-cavities read docking cavities (plus distance grid)
from .as file
-d, --write-insightii-grids dump InsightII grids for each cavity for
visualisation
-v, --write-psf-crd dump target PSF/CRD files for rDock Viewer
-l, --list-atoms-dist arg list receptor atoms within specified distance
of any cavity (in angstrom) (default: 5.0)
-s, --print-site print SITE descriptors (counts of exposed
atoms)
-b, --border arg set the border around the cavities for the
distance grid (in angstrom) (default: 8.0)
-m, --write-moe-grid write active site into a MOE grid
-h, --help Print help
$ rbdock -h
***********************************************
The RxDock molecular docking program is licensed under GNU LGPL version 3.
RxDock is maintained by Vedran Miletić, Patrik Nikolić, and Luka Vretenar.
Visit https://rxdock.gitlab.io/ for more information.
Executable: rbdock/0.1.0
Library: librxdock.so/0.1.0
RBT_ROOT: /home/pnikolic/rxdock
RBT_HOME: /home/pnikolic
Current dir: /home/pnikolic/rxdock
Date: Thu Jan 27 22:03:11 2022
***********************************************
rbdock - docking engine
Usage:
rbdock [OPTION...]
-i, --input arg input ligand SD file
-o, --output arg output file name(s) prefix
-r, --receptor-param arg receptor parameter file
-p, --docking-param arg docking protocol parameter file
-n, --number arg number of runs per ligand (0 = unlimited)
(default: 0)
-P, --protonate protonate all neutral amines, guanidines,
imidazoles
-D, --deprotonate deprotonate all carboxylic, sulphur and
phosphorous acid groups
-H, --all-hydrogens read all hydrogens present instead of only polar
hydrogens
-t, --threshold arg score threshold
-C, --continue continue if score threshold is met instead of
terminating ligand
-f, --filter arg filter file name
-T, --trace arg controls output level for debugging (0 = minimal,
>0 = more verbose) (default: 0)
-s, --seed arg random number seed to use instead of
std::random_device
-h, --help Print help
There are other programs as well. You can follow the
Docking in 3 steps part of the documentation from
here on. Just be careful with -was and -ras parameters for rbcavity
which were removed and replaced with -W and -R, respectively. Don’t
worry too much, if you forget and use -was or -ras, rbcavity will
warn you about the removal and suggest what parameters to use instead.
And that’s it! You have your rDock properly built and your workspace is
properly set up. Just remember that you have to set up your working environment
every time you start working. That means every time you reboot your computer,
log out and then back in, close the terminal and open it again, etc. you have
to write those five lines of code above. To avoid that, you can put them into
your shell configuration (.bashrc file in your home directory, in my case
/home/pnikolic).
Should you have any questions, do not hesitate to reach out to the rDock community on the issue tracker, but please search for similar issues first.
Happy docking!
