OK! I understand.
So I sourced /home/xxr/votca_xtp/bin/VOTCARC.bash,
the content of “type -p csg_map” is right as follows:
/home/xxr/votca_xtp/bin/csg_map
There is occurrence of different error as follows:
xtp_map: error while loading shared libraries: libmkl_core.so: cannot open
shared object file: No such file or directory
-----Original Messages-----
From:"Christoph Junghans" <[email protected]>
Sent Time:2020-04-13 12:23:45 (Monday)
To: "谢信锐" <[email protected]>
Cc: "Baumeier, B." <[email protected]>, "Jens Wehner" <[email protected]>,
"[email protected]" <[email protected]>
Subject: Re: Re: Re: Errors
On Sun, Apr 12, 2020, 20:11 谢信锐 <[email protected]> wrote:
1) I couldn't run it with ./xtp_map, the error is shown as follows:
./xtp_map: error while loading shared libraries: libvotca_xtp.so.7: cannot open
shared object file: No such file or directory
2) the content of “type -p csg_map”
/bin/csg_map
1. and 2. both hint at the fact that something went wrong with sourcing
VOTCARC.bash from 3., libvotca_xtp.so.7 should be in /home/xxr/votca_xtp/lib
and csg_map isn't the one from the installation either. So please try to
source the VOTCARC.bash from 3. again with the full path, i.e. source
/home/xxr/votca_xtp/bin/VOTCARC.bash
And remember you have to do this for each new terminal session again.
Christoph
3)the content of votcarc.bash
#!/usr/bin/env bash
#
# Copyright 2009-2017 The VOTCA Development Team (http://www.votca.org)
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
#
#path is never empty
PATH="/home/xxr/votca_xtp/bin:${PATH}"
#debian wants to have : at the end
MANPATH="/home/xxr/votca_xtp/share/man:${MANPATH}"
LD_LIBRARY_PATH="/home/xxr/votca_xtp/lib${LD_LIBRARY_PATH:+:}${LD_LIBRARY_PATH}"
VOTCASHARE="/home/xxr/votca_xtp/share/votca"
export PATH MANPATH LD_LIBRARY_PATH VOTCASHARE
#bash completion
if [ -n "$BASH_VERSION" ]; then
for comp in "${VOTCASHARE}"/rc/*completion.bash; do
[ -r "$comp" ] && source "$comp"
done
unset comp
fi
-----Original Messages-----
From:"Christoph Junghans" <[email protected]>
Sent Time:2020-04-13 09:53:12 (Monday)
To: "谢信锐" <[email protected]>
Cc: "Baumeier, B." <[email protected]>, "Jens Wehner" <[email protected]>,
"[email protected]" <[email protected]>
Subject: Re: Re: Errors
On Sun, Apr 12, 2020 at 19:40 谢信锐 <[email protected]> wrote:
Hi,
I just followed what you said, but still couldn't run the xtp_map command.
Can you run it directly using “./xtp_map”? Also can you post the content of
your VOTCARC.bash? And the content of “type -p csg_map”?
Christoph
Please see the attachment.
###I also installed the votca-ctp, and could run it without errors.
Thank you!
-----Original Messages-----
From:"Baumeier, B." <[email protected]>
Sent Time:2020-04-12 22:16:39 (Sunday)
To: "谢信锐" <[email protected]>, "Christoph Junghans" <[email protected]>
Cc: "Jens Wehner" <[email protected]>, "[email protected]"
<[email protected]>
Subject: Re: Errors
Can you delete everything, then chose as
prefix=/home/xxr/votca_xtp
Then perform everything as before.
When done installing:
source /home/xxr/votca_xtp/bin/VOTCARC.bash
On 12-04-2020 15:44, 谢信锐 wrote:
I have uploaded the picture of /bin and CMake.log!
-----Original Messages-----
From:"Christoph Junghans" <[email protected]>
Sent Time:2020-04-12 21:07:01 (Sunday)
To: "谢信锐" <[email protected]>
Cc: "Baumeier, B." <[email protected]>, "Jens Wehner" <[email protected]>,
"[email protected]" <[email protected]>
Subject: Re: Re: Re: Re: Re: Re: Errors
What is inside the bin folder?
And place use the mailing when posting your full install log.
Christoph
On Sun, Apr 12, 2020 at 06:15 谢信锐 <[email protected]> wrote:
Hi,
The path of prefix=WHERE/TO/INSTALL/VOTCA consists of following contents:
bin include lib share
#Noting that running csg_xxx -h (such as csg_fmatch -h ) works, but not xtp_map
and so on!
-----Original Messages-----
From:"Baumeier, B." <[email protected]>
Sent Time:2020-04-12 16:48:51 (Sunday)
To: "Jens Wehner" <[email protected]>, "谢信锐" <[email protected]>
Cc: "Christoph Junghans" <[email protected]>, "[email protected]"
<[email protected]>
Subject: Re: Re: Re: Re: Re: Errors
Which path did you chose for prefix=WHERE/TO/INSTALL/VOTCA? And what is in this
path?
Get Outlook for Android
From: 谢信锐 <[email protected]>
Sent: Sunday, April 12, 2020 10:34:34 AM
To: Jens Wehner <[email protected]>
Cc: Christoph Junghans <[email protected]>; Baumeier, B. <[email protected]>;
[email protected] <[email protected]>
Subject: Re: Re: Re: Re: Re: Errors
Hi,
a) As follows, I installed the votca
prefix=WHERE/TO/INSTALL/VOTCA
version=master # or 'stable' or 'v1.4.1'
git clone -b ${version} --recursive https://github.com/votca/votca.git cd votca
mkdir build
cd build
cmake -DBUILD_CSGAPPS=ON -DBUILD_XTP=ON -DCMAKE_INSTALL_PREFIX=${prefix} ..
make -j4
make install
b) I searched the cmake.log and couldn't find it.
c) When I run csg_match -h, command 'csg_match' not found.
Sincerely!
-----Original Messages-----
From:"Jens Wehner" <[email protected]>
Sent Time:2020-04-12 16:22:35 (Sunday)
To: "谢信锐" <[email protected]>
Cc: "Christoph Junghans" <[email protected]>, "Baumeier, B."
<[email protected]>, [email protected]
Subject: Re: Re: Re: Re: Errors
HI,
a) how exactly did you get the latest version of votca?
b) how did you install it? Can you post the cmake logs?
c) what happens if you run csg_match -h ?
Cheers Jens
Am So., 12. Apr. 2020 um 08:51 Uhr schrieb 谢信锐 <[email protected]>:
Hi,
I have installed the latest version of vocta,
the occurrence of error:
I have installed VOTCA toolkit including both csg and xtp. When I run the
xtp_map in the presence of file position of
votca/xtp-tutorials/GROMACS/Methane, there is a error!
xtp_map -t MD_FILES/topol.tpr -c MD_FILES/conf.gro -s system.xml -f state.hdf5
xtp_map: command not found
what I did:
I have sourced the VOTCARC.bash;
xtp_map is in bin/ folder of the installation.
How to address this problem?
Thank you!
-----Original Messages-----
From:"Christoph Junghans" <[email protected]>
Sent Time:2020-04-11 20:55:49 (Saturday)
To: "谢信锐" <[email protected]>
Cc: "Jens Wehner" <[email protected]>, "Baumeier, B." <[email protected]>
Subject: Re: Re: Re: Errors
On Sat, Apr 11, 2020, 06:47 谢信锐 <[email protected]> wrote:
Dear Christoph,
I have sourced the VOTCARC.bash, but the same problem still occurred!
Maybe Jens or Bjorn know, both are cc'ed. Please use reply-all from now on.
Is there an xtp_map in bin/ folder of the installation? What version of VOTCA
are you using?
Also could you please post these kind of question on the mailing list,
[email protected], so that others can learn of from it?
Christoph
-----Original Messages-----
From:"Christoph Junghans" <[email protected]>
Sent Time:2020-04-11 20:13:52 (Saturday)
To: "谢信锐" <[email protected]>
Cc: "Baumeier, B." <[email protected]>
Subject: Re: Re: Errors
On Sat, Apr 11, 2020, 05:58 谢信锐 <[email protected]> wrote:
Hi,
Thank you very much!
I have installed VOTCA toolkit including both csg and xtp. When I run the
xtp_map in the presence of file position of
votca/xtp-tutorials/GROMACS/Methane, there is a error!
xtp_map -t MD_FILES/topol.tpr -c MD_FILES/conf.gro -s system.xml -f state.hdf5
xtp_map: command not found
Have you sourced VOTCARC?
Christoph
I could not figure out what happened, and maybe I shall add some definitive
command to allow that process?
Sincerely!
-----Original Messages-----
From:"Christoph Junghans" <[email protected]>
Sent Time:2020-04-08 20:36:24 (Wednesday)
To: "谢信锐" <[email protected]>
Cc: [email protected]
Subject: Re: Errors
On Wed, Apr 8, 2020 at 02:06 谢信锐 <[email protected]> wrote:
Hi,
I have addressed some of errors, but not for CLANG_FORMAT (required version >=
7.0.1)
-- The following OPTIONAL packages have not been found:
As it says here it is optional, so ignore that and go ahead.
Christoph
* CLANG_FORMAT (required version >= 7.0.1)
-- Configuring done
-- Generating done
-- Build files have been written to: /home/xxr/votca-xtp/votca/build
Shall this missing affect next process of installation?
Sincerely!
Xie Xinrui
Department of Chemistry
Zhejiang University
-----Original Messages-----
From:"谢信锐" <[email protected]>
Sent Time:2020-04-08 13:51:31 (Wednesday)
To: [email protected]
Cc:
Subject: Errors
Hi,
When I installed the CTP of VOTCA, some errors occurred after inputting
cmake -DBUILD_CTP=ON -DCMAKE_INSTALL_PREFIX=${prefix} ..
The details of errors is shown as follows:
Boost version: 1.65.1
-- Found the following Boost libraries:
-- program_options
-- filesystem
-- system
-- Could NOT find MKL (missing: MKL_INCLUDE_DIR MKL_Core_LINK_LIBRARY)
-- Found Eigen3: /usr/lib/cmake/eigen3
-- Checking for module 'sqlite3'
-- No package 'sqlite3' found
CMake Error at
/usr/share/cmake-3.10/Modules/FindPackageHandleStandardArgs.cmake:137 (message):
Could NOT find SQLITE3 (missing: SQLITE3_LIBRARY SQLITE3_INCLUDE_DIR)
Call Stack (most recent call first):
/usr/share/cmake-3.10/Modules/FindPackageHandleStandardArgs.cmake:378
(_FPHSA_FAILURE_MESSAGE)
tools/CMakeModules/FindSQLITE3.cmake:31 (find_package_handle_standard_args)
CMakeLists.txt:78 (_find_package)
tools/src/libtools/CMakeLists.txt:12 (find_package)
-- Configuring incomplete, errors occurred!
I'm not familiar with error handling, and guess that some supporting programs
are missing?
Sincerely!
--
Christoph Junghans
Web: http://www.compphys.de
--
Christoph Junghans
Web: http://www.compphys.de
--
Christoph Junghans
Web: http://www.compphys.de
--
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