Re: [ccp4bb] Fwd: Re: [ccp4bb] coot space bar translate rather slow at host machine but not in virtual machine
That problem has been discussed several times on the coot mailing list.
Currently a workaround is to type:
(set-use-stroke-characters 1)
in scheme console (Calculate Scripting Scheme).
(You can also add it to coot settings).
As a side effect fonts will look worse.
I've just tested a better fix (patch attached) and it seems to work,
It requires compilation from source, so for now use the workaround
above.
Marcin
On Sun, May 17, 2015 at 11:10:41AM -0300, Jorge Iulek wrote:
Thanks Carlos Contreras-Martel and Lu Zuokun for pointing me to check
graphic driver problems (or update them from the vendor, by the way,
controller model Intel HD 4000). Taking some time with this today, I still
feel I will have to study further before making changes.
This poses me yet other question, though maybe it escapes the discussion
list scope, that I must search further: how (and where) different are the
resources used by the virtual machine compared to the host machine, such
that this graphical behavior is different.
Yours,
Jorge
On 05/16/2015 08:39 PM, Jorge Iulek wrote:
Dear all,
My machine has openSuSE 12.3, a lenovo ideadpad with 8 cores (4 are
virutal) and 8 GB memory.
For a number of coot versions in it (including the newest one), coot
answers slowly to rotating, but specially the space bar translate is even
more slow (from residue x to x+1 etc.).
Curiously, in either CentOS or even openSuSE in oracle virtualboxes
(under this openSuSE host), to which I liberate only 1 cpu and only 1 GB
memory, it goes much faster, at a very reasonable speed. How could be
that? In principle I thought that the multicore configuration of the host
machine might be the culprit.
So, for coot tasks, I have been using the virtual machine, but that is
impractical.
The closest to this problem I found was
https://www.mail-archive.com/coot@jiscmail.ac.uk/msg03787.html , but I
could not devise any trial to solve the problem. Even trying the
http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/web/docs/coot.html#Slow-Computer-Configuration
http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/web/docs/coot.html#Slow-Computer-Configuration
configuration did not solve the problem satisfactorily.
I tried to search wider, but could not find other suggestions. Should
you have one, I would be glad to try.
Sincerely yours,
Jorge
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--- src/graphics-info.cc2014-12-02 16:00:08.0 +
+++ src/graphics-info.cc2015-05-18 18:29:45.420807088 +0100
@@ -1920,7 +1920,8 @@
} else {
glRasterPos3f(x,y,z);
- glPushAttrib (GL_LIST_BIT);
+ glPushAttrib (GL_LIST_BIT|GL_ENABLE_BIT);
+ glDisable(GL_FOG);
for (unsigned int i = 0; i s.length(); i++)
glutBitmapCharacter (graphics_info_t::atom_label_font, s[i]);
glPopAttrib();
@@ -4649,7 +4650,8 @@
// GLfloat pink[3] = { 1.0, 0.8, 0.8 };
GLfloat pink[3] = { font_colour.red, font_colour.green,
font_colour.blue };
glColor3fv(pink);
- glPushAttrib (GL_LIST_BIT);
+ glPushAttrib (GL_LIST_BIT|GL_ENABLE_BIT);
+ glDisable(GL_FOG);
void *font = graphics_info_t::atom_label_font;
font = GLUT_BITMAP_TIMES_ROMAN_24;
for (unsigned int i=0; igeneric_texts_p-size(); i++) {
--- src/graphics-ligand-view.cc 2014-09-08 20:54:39.0 +0100
+++ src/graphics-ligand-view.cc 2015-05-18 18:27:23.714796284 +0100
@@ -307,7 +307,8 @@
void
graphics_ligand_atom::bitmap_text(const std::string s) const {
- glPushAttrib (GL_LIST_BIT);
+ glPushAttrib (GL_LIST_BIT|GL_ENABLE_BIT);
+ glDisable(GL_FOG);
for (unsigned int i = 0; i s.length(); i++)
glutBitmapCharacter (GLUT_BITMAP_HELVETICA_10, s[i]);
glPopAttrib();
Re: [ccp4bb] Fwd: Re: [ccp4bb] coot space bar translate rather slow at host machine but not in virtual machine
Thanks Marcin, I thought I'd patched this already some time ago (shortly after you mentioned it to me), but now that I try to find it in the logs, it seems to have been missed/lost. Paul. On 18/05/15 19:00, Marcin Wojdyr wrote: That problem has been discussed several times on the coot mailing list. Currently a workaround is to type: (set-use-stroke-characters 1) in scheme console (Calculate Scripting Scheme). (You can also add it to coot settings). As a side effect fonts will look worse. I've just tested a better fix (patch attached) and it seems to work, It requires compilation from source, so for now use the workaround above. Marcin On Sun, May 17, 2015 at 11:10:41AM -0300, Jorge Iulek wrote: Thanks Carlos Contreras-Martel and Lu Zuokun for pointing me to check graphic driver problems (or update them from the vendor, by the way, controller model Intel HD 4000). Taking some time with this today, I still feel I will have to study further before making changes. This poses me yet other question, though maybe it escapes the discussion list scope, that I must search further: how (and where) different are the resources used by the virtual machine compared to the host machine, such that this graphical behavior is different. Yours, Jorge On 05/16/2015 08:39 PM, Jorge Iulek wrote: Dear all, My machine has openSuSE 12.3, a lenovo ideadpad with 8 cores (4 are virutal) and 8 GB memory. For a number of coot versions in it (including the newest one), coot answers slowly to rotating, but specially the space bar translate is even more slow (from residue x to x+1 etc.). Curiously, in either CentOS or even openSuSE in oracle virtualboxes (under this openSuSE host), to which I liberate only 1 cpu and only 1 GB memory, it goes much faster, at a very reasonable speed. How could be that? In principle I thought that the multicore configuration of the host machine might be the culprit. So, for coot tasks, I have been using the virtual machine, but that is impractical. The closest to this problem I found was https://www.mail-archive.com/coot@jiscmail.ac.uk/msg03787.html , but I could not devise any trial to solve the problem. Even trying the http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/web/docs/coot.html#Slow-Computer-Configuration http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/web/docs/coot.html#Slow-Computer-Configuration configuration did not solve the problem satisfactorily. I tried to search wider, but could not find other suggestions. Should you have one, I would be glad to try. Sincerely yours, Jorge
Re: [ccp4bb] Fwd: Re: [ccp4bb] coot space bar translate rather slow at host machine but not in virtual machine
Dear Marcin, Yes, it worked pretty fine. As for the side effect , I could not, for while, observe any degradation. Thank you very much. Jorge On 05/18/2015 03:00 PM, Marcin Wojdyr wrote: That problem has been discussed several times on the coot mailing list. Currently a workaround is to type: (set-use-stroke-characters 1) in scheme console (Calculate Scripting Scheme). (You can also add it to coot settings). As a side effect fonts will look worse. I've just tested a better fix (patch attached) and it seems to work, It requires compilation from source, so for now use the workaround above. Marcin On Sun, May 17, 2015 at 11:10:41AM -0300, Jorge Iulek wrote: Thanks Carlos Contreras-Martel and Lu Zuokun for pointing me to check graphic driver problems (or update them from the vendor, by the way, controller model Intel HD 4000). Taking some time with this today, I still feel I will have to study further before making changes. This poses me yet other question, though maybe it escapes the discussion list scope, that I must search further: how (and where) different are the resources used by the virtual machine compared to the host machine, such that this graphical behavior is different. Yours, Jorge On 05/16/2015 08:39 PM, Jorge Iulek wrote: Dear all, My machine has openSuSE 12.3, a lenovo ideadpad with 8 cores (4 are virutal) and 8 GB memory. For a number of coot versions in it (including the newest one), coot answers slowly to rotating, but specially the space bar translate is even more slow (from residue x to x+1 etc.). Curiously, in either CentOS or even openSuSE in oracle virtualboxes (under this openSuSE host), to which I liberate only 1 cpu and only 1 GB memory, it goes much faster, at a very reasonable speed. How could be that? In principle I thought that the multicore configuration of the host machine might be the culprit. So, for coot tasks, I have been using the virtual machine, but that is impractical. The closest to this problem I found was https://www.mail-archive.com/coot@jiscmail.ac.uk/msg03787.html , but I could not devise any trial to solve the problem. Even trying the http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/web/docs/coot.html#Slow-Computer-Configuration http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/web/docs/coot.html#Slow-Computer-Configuration configuration did not solve the problem satisfactorily. I tried to search wider, but could not find other suggestions. Should you have one, I would be glad to try. Sincerely yours, Jorge
Re: [ccp4bb] Fwd: Re: [ccp4bb] coot space bar translate rather slow at host machine but not in virtual machine
Dear Jorge, A virtual machine simulates a physical machine based on the host OS. Almost all the hardware resources is simulated by the virtual machine, BIOS,CPU,RAM Of course, all these instruction will finally be carried out by the really hardware. Your action on the guest OS will first be decoded by the virtual machine( actually it's just a programme!), then the host OS...finally to the hardware. This is one reason why program in guest OS usually runs slower than that in host OS. In general, your hardware drivers will have complete support to your OS, like Windows. But in your case, the graphics card driver cannot fully support the linux. That's why you slower machine in the linux. Best regards! Lu zuokun -- 卢作焜 南开大学新生物站A202 At 2015-05-17 22:10:41, Jorge Iulek 051fad3bd595-dmarc-requ...@jiscmail.ac.uk wrote: Thanks Carlos Contreras-Martel and Lu Zuokun for pointing me to check graphic driver problems (or update them from the vendor, by the way, controller model Intel HD 4000). Taking some time with this today, I still feel I will have to study further before making changes. This poses me yet other question, though maybe it escapes the discussion list scope, that I must search further: how (and where) different are the resources used by the virtual machine compared to the host machine, such that this graphical behavior is different. Yours, Jorge On 05/16/2015 08:39 PM, Jorge Iulek wrote: Dear all, My machine has openSuSE 12.3, a lenovo ideadpad with 8 cores (4 are virutal) and 8 GB memory. For a number of coot versions in it (including the newest one), coot answers slowly to rotating, but specially the space bar translate is even more slow (from residue x to x+1 etc.). Curiously, in either CentOS or even openSuSE in oracle virtualboxes (under this openSuSE host), to which I liberate only 1 cpu and only 1 GB memory, it goes much faster, at a very reasonable speed. How could be that? In principle I thought that the multicore configuration of the host machine might be the culprit. So, for coot tasks, I have been using the virtual machine, but that is impractical. The closest to this problem I found was https://www.mail-archive.com/coot@jiscmail.ac.uk/msg03787.html , but I could not devise any trial to solve the problem. Even trying the http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/web/docs/coot.html#Slow-Computer-Configuration configuration did not solve the problem satisfactorily. I tried to search wider, but could not find other suggestions. Should you have one, I would be glad to try. Sincerely yours,Jorge
Re: [ccp4bb] Fwd: Re: [ccp4bb] coot space bar translate rather slow at host machine but not in virtual machine
Hi Jorge May I suggest you try opensuse 13.1 or 13.2 where vendor graphic card drivers are now part of the kernel. I'm just testing now 13.1 with the latest version of Coot and Pymol work well with the native graphic driver. Also you already have some (not the latest ones) coot and pymol versions in the opensuse repositories. All the best Carlos On 05/17/2015 04:10 PM, Jorge Iulek wrote: Thanks Carlos Contreras-Martel and Lu Zuokun for pointing me to check graphic driver problems (or update them from the vendor, by the way, controller model Intel HD 4000). Taking some time with this today, I still feel I will have to study further before making changes. This poses me yet other question, though maybe it escapes the discussion list scope, that I must search further: how (and where) different are the resources used by the virtual machine compared to the host machine, such that this graphical behavior is different. Yours, Jorge On 05/16/2015 08:39 PM, Jorge Iulek wrote: Dear all, My machine has openSuSE 12.3, a lenovo ideadpad with 8 cores (4 are virutal) and 8 GB memory. For a number of coot versions in it (including the newest one), coot answers slowly to rotating, but specially the space bar translate is even more slow (from residue x to x+1 etc.). Curiously, in either CentOS or even openSuSE in oracle virtualboxes (under this openSuSE host), to which I liberate only 1 cpu and only 1 GB memory, it goes much faster, at a very reasonable speed. How could be that? In principle I thought that the multicore configuration of the host machine might be the culprit. So, for coot tasks, I have been using the virtual machine, but that is impractical. The closest to this problem I found was https://www.mail-archive.com/coot@jiscmail.ac.uk/msg03787.html , but I could not devise any trial to solve the problem. Even trying the http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/web/docs/coot.html#Slow-Computer-Configuration http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/web/docs/coot.html#Slow-Computer-Configuration configuration did not solve the problem satisfactorily. I tried to search wider, but could not find other suggestions. Should you have one, I would be glad to try. Sincerely yours, Jorge -- Carlos CONTRERAS MARTEL, Ph.D. (CR1 CNRS) carlos.contreras-mar...@ibs.fr Bacterial Pathogenesis Group Institut de Biologie Structurale UMR5075 CEA-CNRS-Université Joseph Fourier Grenoble 1 IBS 71, avenue des Martyrs CS 10090 38044 Grenoble CEDEX 9 FRANCE tel : (+33) (0)4 57 42 86 41 http://www.ibs.fr/groupes/groupe-pathogenie-bacterienne/?lang=fr http://www.ibs.fr/groups/bacterial-pathogenesis-group/?lang=en
