Re: [Avogadro-devel] [Avogadro-Discuss] XTALOPT hangs if server connection lost
Unfortunately the CLI is not correct! I get: Warning: Optimizer::Update: Error loading structure at /home/ucfbcoh/XTALOPT/C12H12/200GPa//3x00051/ and when I look at that directory I find on the client: ls /home/ucfbcoh/XTALOPT/C12H12/200GPa//3x00051/ 3x00051 job.sh structure.state xtal.in ucfbcoh@tomcat:~/src/xtalopt2/build$ ls /home/ucfbcoh/XTALOPT/C12H12/200GPa//3x00051/3x00051/ job.sh pwscf.save xtal.in xtal.out I had fixed this also long ago, but it is back again. It is storing one directory down. Ron --- Ronald Cohen Geophysical Laboratory Carnegie Institution 5251 Broad Branch Rd., N.W. Washington, D.C. 20015 rco...@carnegiescience.edu office: 202-478-8937 skype: ronaldcohen https://twitter.com/recohen3 https://www.linkedin.com/profile/view?id=163327727 On Fri, Aug 21, 2015 at 1:48 AM, Ronald Cohen rco...@carnegiescience.edu wrote: I switched to the CLI ssh and so far no problems! I guess it is a problem with sshlib. Ron Sent from my iPad On Aug 17, 2015, at 9:41 AM, David Lonie david.lo...@kitware.com wrote: On Fri, Aug 14, 2015 at 4:35 PM, Cohen, Ronald rco...@carnegiescience.edu wrote: I had fixed this in an earlier version but don't remember how. Sometimes the connection to the server or nameserver goes down (about once a day) and I see an error like: SSHConnectionLibSSH::isConnected(): server timeout. SSH error: Failed to resolve hostname legion.rc.ucl.ac.uk (Name or service not known) Cannot connect to ssh server ucfb...@legion.rc.ucl.ac.uk:22 Warning: Cannot connect to ssh server If you're having issues resolving hosts, there's not much that can be done about that from the XtalOpt side of things. Might be VPN related? Dave -- ___ Avogadro-Discuss mailing list avogadro-disc...@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/avogadro-discuss -- ___ Avogadro-devel mailing list Avogadro-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/avogadro-devel
Re: [Avogadro-devel] [Avogadro-Discuss] XTALOPT hangs if server connection lost
I think the attached code I edited fixes this problem.
Ron
---
Ronald Cohen
Geophysical Laboratory
Carnegie Institution
5251 Broad Branch Rd., N.W.
Washington, D.C. 20015
rco...@carnegiescience.edu
office: 202-478-8937
skype: ronaldcohen
https://twitter.com/recohen3
https://www.linkedin.com/profile/view?id=163327727
On Fri, Aug 21, 2015 at 12:08 PM, Cohen, Ronald
rco...@carnegiescience.edu wrote:
Unfortunately the CLI is not correct! I get:
Warning: Optimizer::Update: Error loading structure at
/home/ucfbcoh/XTALOPT/C12H12/200GPa//3x00051/
and when I look at that directory I find on the client:
ls /home/ucfbcoh/XTALOPT/C12H12/200GPa//3x00051/
3x00051 job.sh structure.state xtal.in
ucfbcoh@tomcat:~/src/xtalopt2/build$ ls
/home/ucfbcoh/XTALOPT/C12H12/200GPa//3x00051/3x00051/
job.sh pwscf.save xtal.in xtal.out
I had fixed this also long ago, but it is back again. It is storing
one directory down.
Ron
---
Ronald Cohen
Geophysical Laboratory
Carnegie Institution
5251 Broad Branch Rd., N.W.
Washington, D.C. 20015
rco...@carnegiescience.edu
office: 202-478-8937
skype: ronaldcohen
https://twitter.com/recohen3
https://www.linkedin.com/profile/view?id=163327727
On Fri, Aug 21, 2015 at 1:48 AM, Ronald Cohen
rco...@carnegiescience.edu wrote:
I switched to the CLI ssh and so far no problems! I guess it is a problem
with sshlib.
Ron
Sent from my iPad
On Aug 17, 2015, at 9:41 AM, David Lonie david.lo...@kitware.com wrote:
On Fri, Aug 14, 2015 at 4:35 PM, Cohen, Ronald rco...@carnegiescience.edu
wrote:
I had fixed this in an earlier version but don't remember how.
Sometimes the connection to the server or nameserver goes down (about
once a day) and I see an error like:
SSHConnectionLibSSH::isConnected(): server timeout.
SSH error: Failed to resolve hostname legion.rc.ucl.ac.uk (Name or
service not known)
Cannot connect to ssh server ucfb...@legion.rc.ucl.ac.uk:22
Warning: Cannot connect to ssh server
If you're having issues resolving hosts, there's not much that can be done
about that from the XtalOpt side of things. Might be VPN related?
Dave
--
___
Avogadro-Discuss mailing list
avogadro-disc...@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/avogadro-discuss
/**
SSHConnection - Connection to an ssh server for execution, sftp, etc.
Copyright (C) 2010-2012 by David C. Lonie
This source code is released under the New BSD License, (the License).
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.
***/
#ifdef ENABLE_SSH
#include globalsearch/sshconnection_cli.h
#include globalsearch/sshmanager_cli.h
#include QtCore/QDebug
#include QtCore/QProcess
namespace GlobalSearch {
SSHConnectionCLI::SSHConnectionCLI(SSHManagerCLI *parent)
: SSHConnection(parent)
{
}
SSHConnectionCLI::~SSHConnectionCLI()
{
}
bool SSHConnectionCLI::execute(const QString command,
QString stdout_str,
QString stderr_str,
int exitcode)
{
return this-executeSSH(command, QStringList(),
stdout_str, stderr_str, exitcode);
}
bool SSHConnectionCLI::copyFileToServer(const QString localpath,
const QString remotepath)
{
return this-executeSCPTo(localpath, remotepath);
}
bool SSHConnectionCLI::copyFileFromServer(const QString remotepath,
const QString localpath)
{
return this-executeSCPFrom(remotepath, localpath);
}
bool SSHConnectionCLI::readRemoteFile(const QString filename,
QString contents)
{
return this-executeSSH(cat, QStringList(filename), contents);
}
bool SSHConnectionCLI::removeRemoteFile(const QString filename)
{
return this-executeSSH(rm, QStringList(filename));
}
bool SSHConnectionCLI::copyDirectoryToServer(const QString localpath,
const QString remotepath)
{
QStringList args (-p );
args remotepath;
this-executeSSH(mkdir, args);
QString arg1;
arg1 = remotepath + /.. ;
return this-executeSCPTo(localpath, arg1, QStringList(-r));
}
bool SSHConnectionCLI::copyDirectoryFromServer(const QString remotepath,
const QString localpath)
{
QStringList args (-p );
args
Re: [Avogadro-devel] Symmetry element rendering
On Wed, Aug 19, 2015 at 11:26 AM, Marcus Johansson mcode...@gmail.com wrote: Hi Was wondering if anyone has some input on rendering symmetry elements in Avogadro v2. There is a need for “disc” (mirror plane) and “vector” (rotation axis) geometries as well as alpha in order to make things look good. Im currently using the “cylinder” and “sphere” geometries, but as you can see they are not well suited for the job. For some of the other display types we added factories to create triangle geometry. Many things can be represented by triangle meshes, we made the special cases for spheres because we were using impostors and cylinders because there are lots of them and might want to use impostors in the future. It would be great to consider what primitives might be missing, and either add factories that simply create meshes, or boost them to new primitive types if that makes more sense. I also need to dig into an issue with text rendering on Windows where it appears to be causing crashes in the latest release. It would be great to get symmetry elements in Avogadro 2, thanks for working on this! Thanks, Marcus -- ___ Avogadro-devel mailing list Avogadro-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/avogadro-devel
Re: [Avogadro-devel] Symmetry element rendering
Any chance someone could apply this patch to the avogadro v1 master symmetry extension /libmsym? https://github.com/mcodev31/libmsym/commit/b2945fa8a5d7027f6afd8297af465f61981b9ba3.patch I don’t have a fork and pressed for time. It won’t build with g++ only with clang (requires VLA). Might need to set_target_properties (msym PROPERTIES POSITION_INDEPENDENT_CODE TRUE”) as well in symmetry/CMakeLists.txt. (not working on the arch linux package manager) since libmsym uses the BUILD_SHARED_LIBS flag. On 21 Aug 2015, at 15:47, Marcus D. Hanwell marcus.hanw...@kitware.com wrote: It would be great to consider what primitives might be missing, and either add factories that simply create meshes, or boost them to new primitive types if that makes more sense. I also need to dig into an issue with text rendering on Windows where it appears to be causing crashes in the latest release. Avogadro v1 has a nice transparent partial disc rendering for angles that would be nice for cubic groups, a rectangle would probably be better for the other ones since they have orientation. It would be great to get symmetry elements in Avogadro 2, thanks for working on this! No problem it’s fun. There are some more features coming when I get the time: Selection of symmetrically equivalent atoms (requires selection of atoms). Symmetry locking when moving atoms (requires some way to restrict coordinate changes in plugins) Generation of SALCs from basis functions (requires surface rendering) Determination of irreducible representations and symmetrisation of basis functions from other calculations (proper symmetrisation requires code updates in libmsym). Character table gui. -- ___ Avogadro-devel mailing list Avogadro-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/avogadro-devel
