Re: Re: Re: Re: Errors

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Jens Wehner

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Apr 12, 2020, 4:22:48 AM4/12/20
to 谢信锐, Christoph Junghans, Baumeier, B., vo...@googlegroups.com
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 <2173...@zju.edu.cn>:

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" <jung...@votca.org>
Sent Time:2020-04-11 20:55:49 (Saturday)
To: "谢信锐" <2173...@zju.edu.cn>
Cc: "Jens Wehner" <jensw...@gmail.com>, "Baumeier, B." <B.Bau...@tue.nl>
Subject: Re: Re: Re: Errors



On Sat, Apr 11, 2020, 06:47 谢信锐 <2173...@zju.edu.cn> 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, vo...@googlegroups.com, so that others can learn of from it?

Christoph




-----Original Messages-----
From:"Christoph Junghans" <jung...@votca.org>
Sent Time:2020-04-11 20:13:52 (Saturday)
To: "谢信锐" <2173...@zju.edu.cn>
Cc: "Baumeier, B." <B.Bau...@tue.nl>
Subject: Re: Re: Errors



On Sat, Apr 11, 2020, 05:58 谢信锐 <2173...@zju.edu.cn> 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" <jung...@votca.org>
Sent Time:2020-04-08 20:36:24 (Wednesday)
To: "谢信锐" <2173...@zju.edu.cn>
Cc: de...@votca.org
Subject: Re: Errors



On Wed, Apr 8, 2020 at 02:06 谢信锐 <2173...@zju.edu.cn> 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" <2173...@zju.edu.cn>
Sent Time:2020-04-08 13:51:31 (Wednesday)
To: de...@votca.org
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

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Apr 12, 2020, 9:07:13 AM4/12/20
to 谢信锐, Baumeier, B., Jens Wehner, vo...@googlegroups.com
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 <2173...@zju.edu.cn> 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." <B.Bau...@tue.nl>
Sent Time:2020-04-12 16:48:51 (Sunday)
To: "Jens Wehner" <jensw...@gmail.com>, "谢信锐" <2173...@zju.edu.cn>
Cc: "Christoph Junghans" <jung...@votca.org>, "vo...@googlegroups.com" <vo...@googlegroups.com>

Subject: Re: Re: Re: Re: Re: Errors

Which path did you chose for prefix=WHERE/TO/INSTALL/VOTCA? And what is in this path?

From: 谢信锐 <2173...@zju.edu.cn>
Sent: Sunday, April 12, 2020 10:34:34 AM
To: Jens Wehner <jensw...@gmail.com>
Cc: Christoph Junghans <jung...@votca.org>; Baumeier, B. <B.Bau...@tue.nl>; vo...@googlegroups.com <vo...@googlegroups.com>
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" <jensw...@gmail.com>
Sent Time:2020-04-12 16:22:35 (Sunday)
To: "谢信锐" <2173...@zju.edu.cn>
Cc: "Christoph Junghans" <jung...@votca.org>, "Baumeier, B." <B.Bau...@tue.nl>, vo...@googlegroups.com
Subject: Re: Re: Re: Re: Errors

谢信锐

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Apr 12, 2020, 9:46:46 PM4/12/20
to Baumeier, B., Christoph Junghans, Jens Wehner, vo...@googlegroups.com

Hi,


I just followed what you said, but still couldn't run the xtp_map command.

Please see the attachment.


###I also installed the votca-ctp, and could run it without errors. 


Thank you!


-----Original Messages-----
From:"Baumeier, B." <B.Bau...@tue.nl>
Sent Time:2020-04-12 22:16:39 (Sunday)
To: "谢信锐" <2173...@zju.edu.cn>, "Christoph Junghans" <jung...@votca.org>
Cc: "Jens Wehner" <jensw...@gmail.com>, "vo...@googlegroups.com" <vo...@googlegroups.com>
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" <jung...@votca.org>
Sent Time:2020-04-12 21:07:01 (Sunday)
To: "谢信锐" <2173...@zju.edu.cn>
Cc: "Baumeier, B." <B.Bau...@tue.nl>, "Jens Wehner" <jensw...@gmail.com>, "vo...@googlegroups.com" <vo...@googlegroups.com>
Subject: Re: Re: Re: Re: Re: Re: Errors
votca_xtp.png

Christoph Junghans

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Apr 12, 2020, 9:53:25 PM4/12/20
to 谢信锐, Baumeier, B., Jens Wehner, vo...@googlegroups.com
On Sun, Apr 12, 2020 at 19:40 谢信锐 <2173...@zju.edu.cn> 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 

谢信锐

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Apr 12, 2020, 10:11:55 PM4/12/20
to Christoph Junghans, Baumeier, B., Jens Wehner, vo...@googlegroups.com

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


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" <jung...@votca.org>
Sent Time:2020-04-13 09:53:12 (Monday)

To: "谢信锐" <2173...@zju.edu.cn>
Cc: "Baumeier, B." <B.Bau...@tue.nl>, "Jens Wehner" <jensw...@gmail.com>, "vo...@googlegroups.com" <vo...@googlegroups.com>
Subject: Re: Re: Errors

Christoph Junghans

unread,
Apr 13, 2020, 12:24:00 AM4/13/20
to 谢信锐, Baumeier, B., Jens Wehner, vo...@googlegroups.com


On Sun, Apr 12, 2020, 20:11 谢信锐 <2173...@zju.edu.cn> 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

谢信锐

unread,
Apr 13, 2020, 12:59:34 AM4/13/20
to Christoph Junghans, Baumeier, B., Jens Wehner, vo...@googlegroups.com

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" <jung...@votca.org>
Sent Time:2020-04-13 12:23:45 (Monday)

To: "谢信锐" <2173...@zju.edu.cn>
Cc: "Baumeier, B." <B.Bau...@tue.nl>, "Jens Wehner" <jensw...@gmail.com>, "vo...@googlegroups.com" <vo...@googlegroups.com>
Subject: Re: Re: Re: Errors

谢信锐

unread,
Apr 13, 2020, 4:55:09 AM4/13/20
to Baumeier, B., Christoph Junghans, Jens Wehner, vo...@googlegroups.com

Yes, I figured out it.

When I install MKL, the configuration (mkl.conf) in the file /etc/ld.so.conf.d/ lost. Therefore, I added the mkl.conf, and it worked.


Thank you very much for providing the patient guidance!


Sincerely!



-----Original Messages-----
From:"Baumeier, B." <B.Bau...@tue.nl>
Sent Time:2020-04-13 14:49:40 (Monday)

To: "谢信锐" <2173...@zju.edu.cn>, "Christoph Junghans" <jung...@votca.org>
Cc: "Jens Wehner" <jensw...@gmail.com>, "vo...@googlegroups.com" <vo...@googlegroups.com>
Subject: Re: Re: Re: Re: Errors

This error means that you linked against the MKL but the library is not available in the current shell session. If you source the compiler environment using some „compilervars.sh“ in the compiler‘s bin directory, it should be available.

What did you use to set the intel compiler or MKL environment for compilation?

---
dr. B. (Bjoern) Baumeier
Assistant Professor
Eindhoven University of Technology
Department of Mathematics and Computer Science & Institute for Complex Molecular Systems
P.O. Box 513 - 5600 MB Eindhoven - The Netherlands
Centre for Analysis, Scientific Computing, and Application (Office MF 7.142 and CE 1.44a)
Telephone: +31-(0)40-247-2205
Twitter: @BaumeierGroup
From: 谢信锐 <2173...@zju.edu.cn>
Sent: Monday, April 13, 2020 6:59:18 AM
To: Christoph Junghans <jung...@votca.org>
Cc: Baumeier, B. <B.Bau...@tue.nl>; Jens Wehner <jensw...@gmail.com>; vo...@googlegroups.com <vo...@googlegroups.com>
Subject: Re: Re: Re: Re: Errors
 
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