From kakhaber.jandieri at physik.uni-marburg.de Fri Jan 13 17:00:58 2012 From: kakhaber.jandieri at physik.uni-marburg.de (Kakhaber Jandieri) Date: Fri, 13 Jan 2012 17:00:58 +0100 Subject: [xcrysden] Installation of Xcrysden/Cygwin Message-ID: <20120113170058.142866c4n9svjchs@home.staff.uni-marburg.de> Dear All, I am a new user of XcrysDen. I want to install it on my Windows XP mashine. I downloaded XC-1.5.18-cygwin-shared package and performed the configuration by ./xcConfigure.sh. The ./xcrysden command in cygwin shell gives the following error: could not read file "/cygdrive/c/cygwin/home/jandieri/XCrySDen/Tcl/xcInit.tcl": no such file or directory. I checked - this file exists. Could you give me an advice? What is running wrong? Beforehand thankfull, Kakhaber From kakhaber.jandieri at physik.uni-marburg.de Mon Jan 16 11:21:12 2012 From: kakhaber.jandieri at physik.uni-marburg.de (Kakhaber Jandieri) Date: Mon, 16 Jan 2012 11:21:12 +0100 Subject: [xcrysden] Problem is solved Message-ID: <20120116112112.137733yqd3ua2xvk@home.staff.uni-marburg.de> Dear All, in my previous letter I wrote about the problems due to th installation of xcrysden on Window XP machine. I already solved this problem. Regards, Kakhaber From tone.kokalj at ijs.si Wed Jan 18 14:54:47 2012 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Wed, 18 Jan 2012 14:54:47 +0100 Subject: [xcrysden] XCrysden on OS X via Fink Message-ID: <1326894887.3877.24.camel@catalyst.ijs.si> Hi everybody, I am glad to announce that thanks to an initiative of Ralph Gebauer and realization of Hanspeter Niederstrasser, xcrysden is now available via Fink for OS X 10.7 (64bit build and everything), 10.6, and 10.5. I suppose this means (I can't check it, because I don't have mac) that xcrysden can be installed as: apt-get install xcrysden Best regards, -- Anton Kokalj J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax:+386-1-477-3822) Please, if possible, avoid sending me Word or PowerPoint attachments. See: http://www.gnu.org/philosophy/no-word-attachments.html From d.m.o.heggo at ub.uio.no Fri Jan 20 17:53:34 2012 From: d.m.o.heggo at ub.uio.no (=?UTF-8?Q?Dan_Michael_O=2E_Hegg=C3=B8?=) Date: Fri, 20 Jan 2012 17:53:34 +0100 Subject: [xcrysden] The rapid screen flickering issue on Mac OS X Message-ID: Hi, First I'm very glad to see XCrysDen now compiles quite easily on Mac OS X! (at least when having a rich MacPorts installation) The shared and semishared packages also starts without any library issues on my Mac OS X Lion (10.7.2) installation. But there is an issue in every case... a quite big one... I'm observing the "rapid flicker" issue described earlier here: http://www.democritos.it/pipermail/xcrysden/2011-July/001006.html http://markmail.org/message/zfol72gfbbxnmyox Sadly this makes the program quite unusable. Are there any news on this one? Or ideas about what might cause it? I've updated all macports packages. Thinking perhaps this was an issue with MESA on Mac OS X Lion, I tried running som MESA tests, but they ran fine without any flickering. Also, other X11 apps run fine. And then, curiously when I tried to record my screen using screencapture, the flickering did not show in the recorded movie! But David also noted in one of the mails above that the flickering disappears over VNC, so I guess it's the same (strange) cause behind this. I use mesa @7.11.2_0 otool -L xcrys returns: /opt/local/lib/libfftw3.3.dylib (compatibility version 7.0.0, current version 7.0.0) /opt/local/lib/libmeschach.1.dylib (compatibility version 1.2.0, current version 1.2.0) /opt/local/lib/libtk8.5.dylib (compatibility version 8.5.0, current version 8.5.11) /opt/local/lib/libtcl8.5.dylib (compatibility version 8.5.0, current version 8.5.11) /opt/local/lib/libGLU.1.dylib (compatibility version 1.3.0, current version 1.3.0) /opt/local/lib/libGL.1.dylib (compatibility version 1.2.0, current version 1.2.0) /opt/local/lib/libXmu.6.dylib (compatibility version 9.0.0, current version 9.0.0) /opt/local/lib/libX11.6.dylib (compatibility version 10.0.0, current version 10.0.0) /opt/local/lib/libXext.6.dylib (compatibility version 11.0.0, current version 11.0.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 159.1.0) Best wishes, Dan Michael Hegg? From jxzhu at lanl.gov Fri Jan 20 19:34:11 2012 From: jxzhu at lanl.gov (Zhu, Jian-Xin) Date: Fri, 20 Jan 2012 18:34:11 +0000 Subject: [xcrysden] The rapid screen flickering issue on Mac OS X In-Reply-To: Message-ID: Dan, I have the same horrible problem on my Mac OS X Lion machine. Sometime David once indicated to me that tcl and/or tk could also be a cause. JX -----Original Message----- From: "Dan Michael O. Hegg?" Reply-To: XCrySDen mailing list Date: Fri, 20 Jan 2012 17:53:34 +0100 To: Subject: [xcrysden] The rapid screen flickering issue on Mac OS X >Hi, > >First I'm very glad to see XCrysDen now compiles quite easily on Mac >OS X! (at least when having a rich MacPorts installation) >The shared and semishared packages also starts without any library >issues on my Mac OS X Lion (10.7.2) installation. > >But there is an issue in every case... a quite big one... I'm >observing the "rapid flicker" issue described earlier here: > >http://www.democritos.it/pipermail/xcrysden/2011-July/001006.html >http://markmail.org/message/zfol72gfbbxnmyox > >Sadly this makes the program quite unusable. Are there any news on >this one? Or ideas about what might cause it? I've updated all >macports packages. >Thinking perhaps this was an issue with MESA on Mac OS X Lion, I tried >running som MESA tests, but they ran fine without any flickering. >Also, other X11 apps run fine. > >And then, curiously when I tried to record my screen using >screencapture, the flickering did not show in the recorded movie! But >David also noted in one of the mails above that the flickering >disappears over VNC, so I guess it's the same (strange) cause behind >this. > >I use mesa @7.11.2_0 > >otool -L xcrys returns: > > /opt/local/lib/libfftw3.3.dylib (compatibility version 7.0.0, current >version 7.0.0) > /opt/local/lib/libmeschach.1.dylib (compatibility version 1.2.0, >current version 1.2.0) > /opt/local/lib/libtk8.5.dylib (compatibility version 8.5.0, current >version 8.5.11) > /opt/local/lib/libtcl8.5.dylib (compatibility version 8.5.0, current >version 8.5.11) > /opt/local/lib/libGLU.1.dylib (compatibility version 1.3.0, current >version 1.3.0) > /opt/local/lib/libGL.1.dylib (compatibility version 1.2.0, current >version 1.2.0) > /opt/local/lib/libXmu.6.dylib (compatibility version 9.0.0, current >version 9.0.0) > /opt/local/lib/libX11.6.dylib (compatibility version 10.0.0, current >version 10.0.0) > /opt/local/lib/libXext.6.dylib (compatibility version 11.0.0, current >version 11.0.0) > /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current >version 159.1.0) > > >Best wishes, >Dan Michael Hegg? >_______________________________________________ >XCrySDen mailing list >XCrySDen at democritos.it >http://www.democritos.it/mailman/listinfo/xcrysden From henrik.lofas at fysik.uu.se Mon Jan 23 11:12:37 2012 From: henrik.lofas at fysik.uu.se (=?ISO-8859-1?B?SGVucmlrIEz2ZuVz?=) Date: Mon, 23 Jan 2012 11:12:37 +0100 Subject: [xcrysden] The rapid screen flickering issue on Mac OS X In-Reply-To: References: Message-ID: I have tried the new xcrysden available via fink on Mac OS X Lion. It works like a charm then. So probably there is some issues with external libraries. Regards Henrik 2012/1/20 Zhu, Jian-Xin > Dan, > > I have the same horrible problem on my Mac OS X Lion machine. > Sometime David once indicated to me that tcl and/or tk could also be a > cause. > > JX > > > > -----Original Message----- > From: "Dan Michael O. Hegg?" > Reply-To: XCrySDen mailing list > Date: Fri, 20 Jan 2012 17:53:34 +0100 > To: > Subject: [xcrysden] The rapid screen flickering issue on Mac OS X > > >Hi, > > > >First I'm very glad to see XCrysDen now compiles quite easily on Mac > >OS X! (at least when having a rich MacPorts installation) > >The shared and semishared packages also starts without any library > >issues on my Mac OS X Lion (10.7.2) installation. > > > >But there is an issue in every case... a quite big one... I'm > >observing the "rapid flicker" issue described earlier here: > > > >http://www.democritos.it/pipermail/xcrysden/2011-July/001006.html > >http://markmail.org/message/zfol72gfbbxnmyox > > > >Sadly this makes the program quite unusable. Are there any news on > >this one? Or ideas about what might cause it? I've updated all > >macports packages. > >Thinking perhaps this was an issue with MESA on Mac OS X Lion, I tried > >running som MESA tests, but they ran fine without any flickering. > >Also, other X11 apps run fine. > > > >And then, curiously when I tried to record my screen using > >screencapture, the flickering did not show in the recorded movie! But > >David also noted in one of the mails above that the flickering > >disappears over VNC, so I guess it's the same (strange) cause behind > >this. > > > >I use mesa @7.11.2_0 > > > >otool -L xcrys returns: > > > > /opt/local/lib/libfftw3.3.dylib (compatibility version 7.0.0, > current > >version 7.0.0) > > /opt/local/lib/libmeschach.1.dylib (compatibility version 1.2.0, > >current version 1.2.0) > > /opt/local/lib/libtk8.5.dylib (compatibility version 8.5.0, current > >version 8.5.11) > > /opt/local/lib/libtcl8.5.dylib (compatibility version 8.5.0, > current > >version 8.5.11) > > /opt/local/lib/libGLU.1.dylib (compatibility version 1.3.0, current > >version 1.3.0) > > /opt/local/lib/libGL.1.dylib (compatibility version 1.2.0, current > >version 1.2.0) > > /opt/local/lib/libXmu.6.dylib (compatibility version 9.0.0, current > >version 9.0.0) > > /opt/local/lib/libX11.6.dylib (compatibility version 10.0.0, > current > >version 10.0.0) > > /opt/local/lib/libXext.6.dylib (compatibility version 11.0.0, > current > >version 11.0.0) > > /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current > >version 159.1.0) > > > > > >Best wishes, > >Dan Michael Hegg? > >_______________________________________________ > >XCrySDen mailing list > >XCrySDen at democritos.it > >http://www.democritos.it/mailman/listinfo/xcrysden > > _______________________________________________ > XCrySDen mailing list > XCrySDen at democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20120123/4001db66/attachment.htm From tone.kokalj at ijs.si Mon Jan 23 11:34:29 2012 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Mon, 23 Jan 2012 11:34:29 +0100 Subject: [xcrysden] The rapid screen flickering issue on Mac OS X Message-ID: <1327314869.3134.16.camel@catalyst.ijs.si> Concerning the rapid screen flickering issue on Mac OS X, I forward the email of the Hanspeter Niederstrasser, who have managed the xcrysden @ fink. -------- Forwarded Message -------- > From: Hanspeter Niederstrasser > To: tone.kokalj at ijs.si > Cc: "Dan Michael O. Hegg?" > Subject: Re: [Fwd: [xcrysden] The rapid screen flickering issue on Mac > OS X] > Date: Fri, 20 Jan 2012 12:39:06 -0500 > > That user is using MacPorts (a different OS X package manager from Fink) > and it's probable that their libraries are built with different > settings. A quick glance shows that MacPorts uses mesa-7.11.2 and Fink > has the older 7.0.2, so it might be due to version issues. Fink is > still on an older version for historical reasons. > > I definitely don't see any flickering in xcrysden here with the Fink > install on 10.7. The only quick issue I noticed when loading one of the > sample files was that turning on aliasing made the dragging and rotating > very slow, but I think that's primarily a lack of hardware acceleration. > No flickering though. > > I would advise the user (CC'd) to ask the MacPorts mesa maintainer as he > might know more about a cause or workaround. If he wants to invest the > time, he could also try installing xcrysden through Fink to see if the > flicker disappears so a hardware issue can be eliminated as a > possibility . But building all of xcrysden's dependencies from scratch > (esp gcc46) for just a test is quite an undertaking. > > Hanspeter -- Anton Kokalj J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax:+386-1-477-3822) Please, if possible, avoid sending me Word or PowerPoint attachments. See: http://www.gnu.org/philosophy/no-word-attachments.html From d.m.o.heggo at ub.uio.no Mon Jan 23 21:30:09 2012 From: d.m.o.heggo at ub.uio.no (=?UTF-8?Q?Dan_Michael_O=2E_Hegg=C3=B8?=) Date: Mon, 23 Jan 2012 21:30:09 +0100 Subject: [xcrysden] The rapid screen flickering issue on Mac OS X In-Reply-To: <1327314869.3134.16.camel@catalyst.ijs.si> References: <1327314869.3134.16.camel@catalyst.ijs.si> Message-ID: Thanks for pointing me in the right direction! I tried replacing mesa-7.11.2 with mesa-7.0.2, and with everything else being equal, the flickering issue then disappeared (I even tried swapping mesa-7.11.2 back again, and there the flickering was back again. So it's related to some changes in mesa between version 7.0.2 and 7.11.2. Just for testing, I tried building some intermediate versions (7.0.4, 7.1 and 7.2), but neither built easily, and I didn't want to spend a lot of time on that. I'm not really sure how to follow this up. In case anyone's interested in having mesa-7.0.2 installed through macports, my modified portfile for mesa-7.0.2 is here: https://gist.github.com/1658983 It can be put in a local repo, that will take precedence over the remote repo, which can be quite useful: http://guide.macports.org/#development.local-repositories Dan Michael On 23 January 2012 11:34, Tone Kokalj wrote: > > Concerning the rapid screen flickering issue on Mac OS X, I forward the > email of the Hanspeter Niederstrasser, who have managed the xcrysden @ > fink. > > -------- Forwarded Message -------- >> From: Hanspeter Niederstrasser >> To: tone.kokalj at ijs.si >> Cc: "Dan Michael O. Hegg?" >> Subject: Re: [Fwd: [xcrysden] The rapid screen flickering issue on Mac >> OS X] >> Date: Fri, 20 Jan 2012 12:39:06 -0500 >> >> That user is using MacPorts (a different OS X package manager from Fink) >> and it's probable that their libraries are built with different >> settings. ?A quick glance shows that MacPorts uses mesa-7.11.2 and Fink >> has the older 7.0.2, so it might be due to version issues. ?Fink is >> still on an older version for historical reasons. >> >> I definitely don't see any flickering in xcrysden here with the Fink >> install on 10.7. ?The only quick issue I noticed when loading one of the >> sample files was that turning on aliasing made the dragging and rotating >> very slow, but I think that's primarily a lack of hardware acceleration. >> ? No flickering though. >> >> I would advise the user (CC'd) to ask the MacPorts mesa maintainer as he >> might know more about a cause or workaround. ?If he wants to invest the >> time, he could also try installing xcrysden through Fink to see if the >> flicker disappears so a hardware issue can be eliminated as a >> possibility . ?But building all of xcrysden's dependencies from scratch >> (esp gcc46) for just a test is quite an undertaking. >> >> Hanspeter > > -- > Anton Kokalj > J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia > (tel: +386-1-477-3523 // fax:+386-1-477-3822) > > Please, if possible, avoid sending me Word or PowerPoint attachments. > See: ?http://www.gnu.org/philosophy/no-word-attachments.html > > _______________________________________________ > XCrySDen mailing list > XCrySDen at democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden From jxzhu at lanl.gov Mon Jan 23 22:47:33 2012 From: jxzhu at lanl.gov (Zhu, Jian-Xin) Date: Mon, 23 Jan 2012 21:47:33 +0000 Subject: [xcrysden] The rapid screen flickering issue on Mac OS X In-Reply-To: Message-ID: Hi Dan, Thanks for sharing your experience here. I would like to use your portfile for mesa-7.0.2 into MacPorts. To fulfill this purpose, I put your Portfile a local directory /Users/Admin/ports/x11/mesa and modify the sources.conf file as follows file:///Users/Admin/ports/x11/mesa rsync://rsync.macports.org/release/tarballs/ports.tar [default] By executing sudo port install mesa, I got the following problem Warning: Can't open index file for source: file:///Users/Admin/ports Error: Port mesa not found I have also tried the following to no avail. file:///Users/Admin/ports/x11/mesa rsync://rsync.macports.org/release/tarballs/ports.tar [default] Password: Warning: Can't open index file for source: file:///Users/Admin/ports/x11/mesa Warning: Skipping mesa (not in the ports tree) The command pwd shows a correct path /Users/Admin/ports/x11/mesa Any help will be greatly appreciated. Thanks, Jian-Xin -----Original Message----- From: "Dan Michael O. Hegg?" Reply-To: XCrySDen mailing list Date: Mon, 23 Jan 2012 21:30:09 +0100 To: XCrySDen mailing list Subject: Re: [xcrysden] The rapid screen flickering issue on Mac OS X >Thanks for pointing me in the right direction! > >I tried replacing mesa-7.11.2 with mesa-7.0.2, and with everything >else being equal, the flickering issue then disappeared (I even tried >swapping mesa-7.11.2 back again, and there the flickering was back >again. So it's related to some changes in mesa between version 7.0.2 >and 7.11.2. Just for testing, I tried building some intermediate >versions (7.0.4, 7.1 and 7.2), but neither built easily, and I didn't >want to spend a lot of time on that. I'm not really sure how to follow >this up. > >In case anyone's interested in having mesa-7.0.2 installed through >macports, my modified portfile for mesa-7.0.2 is here: >https://gist.github.com/1658983 >It can be put in a local repo, that will take precedence over the >remote repo, which can be quite useful: >http://guide.macports.org/#development.local-repositories > >Dan Michael > > >On 23 January 2012 11:34, Tone Kokalj wrote: >> >> Concerning the rapid screen flickering issue on Mac OS X, I forward the >> email of the Hanspeter Niederstrasser, who have managed the xcrysden @ >> fink. >> >> -------- Forwarded Message -------- >>> From: Hanspeter Niederstrasser >>> To: tone.kokalj at ijs.si >>> Cc: "Dan Michael O. Hegg?" >>> Subject: Re: [Fwd: [xcrysden] The rapid screen flickering issue on Mac >>> OS X] >>> Date: Fri, 20 Jan 2012 12:39:06 -0500 >>> >>> That user is using MacPorts (a different OS X package manager from >>>Fink) >>> and it's probable that their libraries are built with different >>> settings. A quick glance shows that MacPorts uses mesa-7.11.2 and Fink >>> has the older 7.0.2, so it might be due to version issues. Fink is >>> still on an older version for historical reasons. >>> >>> I definitely don't see any flickering in xcrysden here with the Fink >>> install on 10.7. The only quick issue I noticed when loading one of >>>the >>> sample files was that turning on aliasing made the dragging and >>>rotating >>> very slow, but I think that's primarily a lack of hardware >>>acceleration. >>> No flickering though. >>> >>> I would advise the user (CC'd) to ask the MacPorts mesa maintainer as >>>he >>> might know more about a cause or workaround. If he wants to invest the >>> time, he could also try installing xcrysden through Fink to see if the >>> flicker disappears so a hardware issue can be eliminated as a >>> possibility . But building all of xcrysden's dependencies from scratch >>> (esp gcc46) for just a test is quite an undertaking. >>> >>> Hanspeter >> >> -- >> Anton Kokalj >> J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia >> (tel: +386-1-477-3523 // fax:+386-1-477-3822) >> >> Please, if possible, avoid sending me Word or PowerPoint attachments. >> See: http://www.gnu.org/philosophy/no-word-attachments.html >> >> _______________________________________________ >> XCrySDen mailing list >> XCrySDen at democritos.it >> http://www.democritos.it/mailman/listinfo/xcrysden >_______________________________________________ >XCrySDen mailing list >XCrySDen at democritos.it >http://www.democritos.it/mailman/listinfo/xcrysden From jxzhu at lanl.gov Mon Jan 23 23:14:06 2012 From: jxzhu at lanl.gov (Zhu, Jian-Xin) Date: Mon, 23 Jan 2012 22:14:06 +0000 Subject: [xcrysden] The rapid screen flickering issue on Mac OS X In-Reply-To: Message-ID: Hi Dan, As a followup to my previous email, it looks I should have run "portindex" under /Users/Admin/ports rather than under /Users/Admin/ports/x11/mesa But I got the error during the "sudo port install mesa" stage ?. To make python 2.7 the default (i.e. the version you get when you run 'python'), please run: sudo port select --set python python27 ---> Cleaning python27 ---> Computing dependencies for mesa could not read "/Users/Admin/ports/x11/mesa/Portfile": permission denied Error: Status 1 encountered during processing. To report a bug, see I don't see there is a permission problem. ~/ports/x11/mesa] Admin% ls -al total 16 drwxr-xr-x 4 Admin staff 136 Jan 23 15:11 ./ drwxr-xr-x 3 Admin staff 102 Jan 23 14:15 ../ -rw-r--r-- 1 Admin staff 2531 Jan 22 14:39 Portfile lrwxr-xr-x 1 root staff 67 Jan 23 15:01 work@ -> /opt/local/var/macports/build/_Users_Admin_ports_x11_mesa/mesa/work Thanks for the help. Jian-Xin -----Original Message----- From: "Dan Michael O. Hegg?" Reply-To: XCrySDen mailing list Date: Mon, 23 Jan 2012 21:30:09 +0100 To: XCrySDen mailing list Subject: Re: [xcrysden] The rapid screen flickering issue on Mac OS X >Thanks for pointing me in the right direction! > >I tried replacing mesa-7.11.2 with mesa-7.0.2, and with everything >else being equal, the flickering issue then disappeared (I even tried >swapping mesa-7.11.2 back again, and there the flickering was back >again. So it's related to some changes in mesa between version 7.0.2 >and 7.11.2. Just for testing, I tried building some intermediate >versions (7.0.4, 7.1 and 7.2), but neither built easily, and I didn't >want to spend a lot of time on that. I'm not really sure how to follow >this up. > >In case anyone's interested in having mesa-7.0.2 installed through >macports, my modified portfile for mesa-7.0.2 is here: >https://gist.github.com/1658983 >It can be put in a local repo, that will take precedence over the >remote repo, which can be quite useful: >http://guide.macports.org/#development.local-repositories > >Dan Michael > > >On 23 January 2012 11:34, Tone Kokalj wrote: >> >> Concerning the rapid screen flickering issue on Mac OS X, I forward the >> email of the Hanspeter Niederstrasser, who have managed the xcrysden @ >> fink. >> >> -------- Forwarded Message -------- >>> From: Hanspeter Niederstrasser >>> To: tone.kokalj at ijs.si >>> Cc: "Dan Michael O. Hegg?" >>> Subject: Re: [Fwd: [xcrysden] The rapid screen flickering issue on Mac >>> OS X] >>> Date: Fri, 20 Jan 2012 12:39:06 -0500 >>> >>> That user is using MacPorts (a different OS X package manager from >>>Fink) >>> and it's probable that their libraries are built with different >>> settings. A quick glance shows that MacPorts uses mesa-7.11.2 and Fink >>> has the older 7.0.2, so it might be due to version issues. Fink is >>> still on an older version for historical reasons. >>> >>> I definitely don't see any flickering in xcrysden here with the Fink >>> install on 10.7. The only quick issue I noticed when loading one of >>>the >>> sample files was that turning on aliasing made the dragging and >>>rotating >>> very slow, but I think that's primarily a lack of hardware >>>acceleration. >>> No flickering though. >>> >>> I would advise the user (CC'd) to ask the MacPorts mesa maintainer as >>>he >>> might know more about a cause or workaround. If he wants to invest the >>> time, he could also try installing xcrysden through Fink to see if the >>> flicker disappears so a hardware issue can be eliminated as a >>> possibility . But building all of xcrysden's dependencies from scratch >>> (esp gcc46) for just a test is quite an undertaking. >>> >>> Hanspeter >> >> -- >> Anton Kokalj >> J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia >> (tel: +386-1-477-3523 // fax:+386-1-477-3822) >> >> Please, if possible, avoid sending me Word or PowerPoint attachments. >> See: http://www.gnu.org/philosophy/no-word-attachments.html >> >> _______________________________________________ >> XCrySDen mailing list >> XCrySDen at democritos.it >> http://www.democritos.it/mailman/listinfo/xcrysden >_______________________________________________ >XCrySDen mailing list >XCrySDen at democritos.it >http://www.democritos.it/mailman/listinfo/xcrysden From d.m.o.heggo at ub.uio.no Mon Jan 23 23:40:54 2012 From: d.m.o.heggo at ub.uio.no (=?UTF-8?Q?Dan_Michael_O=2E_Hegg=C3=B8?=) Date: Mon, 23 Jan 2012 23:40:54 +0100 Subject: [xcrysden] The rapid screen flickering issue on Mac OS X In-Reply-To: References: Message-ID: The first line in sources.conf should point to the repo root, i.e. file:///Users/Admin/ports (not including x11/mesa), but I'm not sure if that's causing your problem. Please reply to me in private if this is not helping, as I don't think this is very relevant for the other users on the mailing list. Dan Michael On 23 January 2012 23:14, Zhu, Jian-Xin wrote: > Hi Dan, > > As a followup to my previous email, it looks I should have run "portindex" > under /Users/Admin/ports rather than under /Users/Admin/ports/x11/mesa > > But I got the error during the "sudo port install mesa" stage > > ?. > To make python 2.7 the default (i.e. the version you get when you run > 'python'), please run: > ? ? ? ?sudo port select --set python python27 > > ---> ?Cleaning python27 > ---> ?Computing dependencies for mesa > could not read "/Users/Admin/ports/x11/mesa/Portfile": permission denied > Error: Status 1 encountered during processing. > To report a bug, see > > > > I don't see there is a permission problem. > > ~/ports/x11/mesa] Admin% ls -al > total 16 > drwxr-xr-x ?4 Admin ?staff ? 136 Jan 23 15:11 ./ > drwxr-xr-x ?3 Admin ?staff ? 102 Jan 23 14:15 ../ > -rw-r--r-- ?1 Admin ?staff ?2531 Jan 22 14:39 Portfile > lrwxr-xr-x ?1 root ? staff ? ?67 Jan 23 15:01 work@ -> > /opt/local/var/macports/build/_Users_Admin_ports_x11_mesa/mesa/work > > Thanks for the help. > > Jian-Xin > > > > > > > -----Original Message----- > From: "Dan Michael O. Hegg?" > Reply-To: XCrySDen mailing list > Date: Mon, 23 Jan 2012 21:30:09 +0100 > To: XCrySDen mailing list > Subject: Re: [xcrysden] The rapid screen flickering issue on Mac OS X > >>Thanks for pointing me in the right direction! >> >>I tried replacing mesa-7.11.2 with mesa-7.0.2, and with everything >>else being equal, the flickering issue then disappeared (I even tried >>swapping mesa-7.11.2 back again, and there the flickering was back >>again. So it's related to some changes in mesa between version 7.0.2 >>and 7.11.2. Just for testing, I tried building some intermediate >>versions (7.0.4, 7.1 and 7.2), but neither built easily, and I didn't >>want to spend a lot of time on that. I'm not really sure how to follow >>this up. >> >>In case anyone's interested in having mesa-7.0.2 installed through >>macports, my modified portfile for mesa-7.0.2 is here: >>https://gist.github.com/1658983 >>It can be put in a local repo, that will take precedence over the >>remote repo, which can be quite useful: >>http://guide.macports.org/#development.local-repositories >> >>Dan Michael >> >> >>On 23 January 2012 11:34, Tone Kokalj wrote: >>> >>> Concerning the rapid screen flickering issue on Mac OS X, I forward the >>> email of the Hanspeter Niederstrasser, who have managed the xcrysden @ >>> fink. >>> >>> -------- Forwarded Message -------- >>>> From: Hanspeter Niederstrasser >>>> To: tone.kokalj at ijs.si >>>> Cc: "Dan Michael O. Hegg?" >>>> Subject: Re: [Fwd: [xcrysden] The rapid screen flickering issue on Mac >>>> OS X] >>>> Date: Fri, 20 Jan 2012 12:39:06 -0500 >>>> >>>> That user is using MacPorts (a different OS X package manager from >>>>Fink) >>>> and it's probable that their libraries are built with different >>>> settings. ?A quick glance shows that MacPorts uses mesa-7.11.2 and Fink >>>> has the older 7.0.2, so it might be due to version issues. ?Fink is >>>> still on an older version for historical reasons. >>>> >>>> I definitely don't see any flickering in xcrysden here with the Fink >>>> install on 10.7. ?The only quick issue I noticed when loading one of >>>>the >>>> sample files was that turning on aliasing made the dragging and >>>>rotating >>>> very slow, but I think that's primarily a lack of hardware >>>>acceleration. >>>> ? No flickering though. >>>> >>>> I would advise the user (CC'd) to ask the MacPorts mesa maintainer as >>>>he >>>> might know more about a cause or workaround. ?If he wants to invest the >>>> time, he could also try installing xcrysden through Fink to see if the >>>> flicker disappears so a hardware issue can be eliminated as a >>>> possibility . ?But building all of xcrysden's dependencies from scratch >>>> (esp gcc46) for just a test is quite an undertaking. >>>> >>>> Hanspeter >>> >>> -- >>> Anton Kokalj >>> J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia >>> (tel: +386-1-477-3523 // fax:+386-1-477-3822) >>> >>> Please, if possible, avoid sending me Word or PowerPoint attachments. >>> See: ?http://www.gnu.org/philosophy/no-word-attachments.html >>> >>> _______________________________________________ >>> XCrySDen mailing list >>> XCrySDen at democritos.it >>> http://www.democritos.it/mailman/listinfo/xcrysden >>_______________________________________________ >>XCrySDen mailing list >>XCrySDen at democritos.it >>http://www.democritos.it/mailman/listinfo/xcrysden > > _______________________________________________ > XCrySDen mailing list > XCrySDen at democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden From m.a.mohammadi86 at gmail.com Wed Jan 25 19:51:02 2012 From: m.a.mohammadi86 at gmail.com (mohammad ali mohammadi) Date: Wed, 25 Jan 2012 22:21:02 +0330 Subject: [xcrysden] make.sys Message-ID: hi Im using ubuntu 11.04 64 bit intel(R) celeron(R) I use this : CFLAGS = -ansi -funroll-loops -fPIC -DUSE_FONTS CC = gcc #LDLIB = -ldl MATH = -lm FFLAGS = -O2 FC = gfortran and when make all ,this error occurs: gcc -ansi -funroll-loops -fPIC -DUSE_FONTS -DUSE_FONTS -I/home/mohammad/XCrySDen-1.5.24-src-all/external/src/tcl8.5.9/generic -I/home/mohammad/XCrySDen-1.5.24-src-all/external/src/tk8.5.9/generic -I/home/mohammad/XCrySDen-1.5.24-src-all/external/include -I/usr/include -c shank_Hinv.c shank_Hinv.c:7:27: error: ?M_PI? undeclared here (not in a function) make[2]: *** [shank_Hinv.o] Error 1 make[2]: Leaving directory `/home/mohammad/XCrySDen-1.5.24-src-all/C' make[1]: *** [compile] Error 2 make[1]: Leaving directory `/home/mohammad/XCrySDen-1.5.24-src-all/C' make: *** [src-C] Error 2 pleas help me :( best regards -- M.Ali.Mohammadi -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20120125/afb70b37/attachment.htm From tone.kokalj at ijs.si Fri Jan 27 14:46:33 2012 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Fri, 27 Jan 2012 14:46:33 +0100 Subject: [xcrysden] make.sys In-Reply-To: References: Message-ID: <1327671993.3895.24.camel@catalyst.ijs.si> On Wed, 2012-01-25 at 22:21 +0330, mohammad ali mohammadi wrote: > and when make all ,this error occurs: > > gcc -ansi -funroll-loops -fPIC -DUSE_FONTS -DUSE_FONTS > -I/home/mohammad/XCrySDen-1.5.24-src-all/external/src/tcl8.5.9/generic > -I/home/mohammad/XCrySDen-1.5.24-src-all/external/src/tk8.5.9/generic > -I/home/mohammad/XCrySDen-1.5.24-src-all/external/include > -I/usr/include -c shank_Hinv.c > shank_Hinv.c:7:27: error: ?M_PI? undeclared here (not in a function) The easiest is to define the M_PI in the C/shank_Hinv.c file. Edit the file and insert: #define M_PI 3.14159265358979323846 before the line: const double two_pi = 2.0*M_PI; Regards, Tone -- Anton Kokalj J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax:+386-1-477-3822) Please, if possible, avoid sending me Word or PowerPoint attachments. See: http://www.gnu.org/philosophy/no-word-attachments.html From bogus@does.not.exist.com Tue Jan 3 18:43:30 2012 From: bogus@does.not.exist.com () Date: Tue, 03 Jan 2012 17:43:30 -0000 Subject: No subject Message-ID: tcl/tk (i.e. COMPILE_TCLTK = yes) and it is seems to be the source of problem. Try the system libraries instead, i.e., specify COMPILE_TCLTK = no in Make.sys or even COMPILE_ALL = no (which will prevent the compilation of tcl/tk, mesa & fftw3). Regards, Tone -- Anton Kokalj J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax:+386-1-477-3822) Please, if possible, avoid sending me Word or PowerPoint attachments. See: http://www.gnu.org/philosophy/no-word-attachments.html From bogus@does.not.exist.com Tue Jan 3 18:43:30 2012 From: bogus@does.not.exist.com () Date: Tue, 03 Jan 2012 17:43:30 -0000 Subject: No subject Message-ID: directory inside my cygwin directory, i.e. in /cygwin/home/Utente, then, in ~/xcrysden-1.5.53-bin-cygwin/scripts, i run ./xcConfigure.sh. Finally i source .bashrc. Then, giving the command xcrysden, i get the following message: /home/Utente/xcrysden-1.5.53-bin-cygwin/xcrysden: line 230: /home/Utente/xcrysden-1.5.53-bin-cygwin/bin/xcrys: Bad address Line 230 of file xcrysden is immediately after this line: ${XCRYSDEN_XCRYS_DIR}/xcrys \ In a previous line of the same file, XCRYSDEN_XCRYS_DIR was defined as: if test ! -z $XCRYSDEN_LIB_BINDIR; then XCRYSDEN_XCRYS_DIR=$XCRYSDEN_LIB_BINDIR else XCRYSDEN_XCRYS_DIR=$XCRYSDEN_TOPDIR/bin fi Now, in my case, $XCRYSDEN_TOPDIR/bin is /home/Utente/xcrysden-1.5.53-bin-cygwin/bin/ (in fact this is also the dir. mentioned in the error message). In this directory i have an xcrys.exe file, and no xcrys file, so i tried changing ${XCRYSDEN_XCRYS_DIR}/xcrys to ${XCRYSDEN_XCRYS_DIR}/xcrys.exe, at line 231 of xcrysden file, but this way the xcrysden command gives the following error(s): /home/Utente/xcrysden-1.5.53-bin-cygwin/xcrysden: line 2: $'\r': command not found /home/Utente/xcrysden-1.5.53-bin-cygwin/xcrysden: line 14: $'\r': command not found /home/Utente/xcrysden-1.5.53-bin-cygwin/xcrysden: line 16: $'\r': command not found /home/Utente/xcrysden-1.5.53-bin-cygwin/xcrysden: line 17: warning: setlocale: L)_ALL: cannot change locale (C ': not a valid identifier.53-bin-cygwin/xcrysden: line 18: export: `LC_ALL /home/Utente/xcrysden-1.5.53-bin-cygwin/xcrysden: line 19: $'\r': command not found /home/Utente/xcrysden-1.5.53-bin-cygwin/xcrysden: line 21: $'\r': command not found /home/Utente/xcrysden-1.5.53-bin-cygwin/xcrysden: line 22: $'\r': command not found /home/Utente/xcrysden-1.5.53-bin-cygwin/xcrysden: line 25: syntax error near unexpected token `$'{\r'' 'home/Utente/xcrysden-1.5.53-bin-cygwin/xcrysden: line 25: ` readlink() { I'm new to cygwin (it's the first time i install and use it), so i'm not sure if it's a problem with xcrysden installation or with cygwin (however cygwin terminals seem to work without problems) Does anyone have any hint on how to solve this? many thanks in advance best Elena Elena Molteni Department of Physics University of Milan via Celoria, 16 I-20133, Milan, Italy and European Theoretical Spectroscopy Facility (ETSF) http://www.etsf.eu