From sylvain at bic.mni.mcgill.ca Tue Dec 8 16:15:11 2009 From: sylvain at bic.mni.mcgill.ca (Sylvain Milot) Date: Tue, 8 Dec 2009 16:15:11 -0500 (EST) Subject: [MINC-development] postf problem on grumio [Fwd: RE: help with making pictures of activation] In-Reply-To: <4B1EB38A.105@bic.mni.mcgill.ca> References: <4B1EB38A.105@bic.mni.mcgill.ca> Message-ID: Hi Mike, I tested on 3 systems so far and it segfaults on all 3 - and for both /usr/local/bic/bin/postf and /usr/local/mni/bin/postf. I also tried with different data. I have CC'ed minc-development but I don't know if this software is actually supported. S On Tue, 8 Dec 2009, Michael Ferreira wrote: > Hello again admins, > > I just verified this problem w/ postf myself. Basically trying to open any > Minc image w/ postf on grumio results in a Seg Fault: > > grumio: /data/scratch/scratch1/mferre % postf test2.mnc > Getting image information ... done > Reading minc data ...................................... done > Segmentation fault > > It works fine on our Linux workstations. > > mike > > > > -------- Original Message -------- > Subject: RE: help with making pictures of activation > Date: Sun, 6 Dec 2009 16:32:52 -0500 > From: Lana Depatie > To: Michael Ferreira > > Hi Mike, > > I tried to log in the bic (i.e., login.bic.mni.mcgill.ca) and to type the > following command in the directory where my file was (cd > /data/szrisk/szrisk2/lana/icbm_june/anal/as-vgs/adhd-i: "postf > adhd-i_as-vgs_t.mnc". > > I get the following messages: > "Getting image information .... done" > "Reading minc data ...done" > "Segmentation fault" > and then I get back to the prompt. > > Do you know what the problem is? > Thanks > --- Sylvain Milot (sylvain at bic.mni.mcgill.ca) (bicadmin at bic.mni.mcgill.ca) Brain Imaging Centre Montreal Neurological Institute 3801 University Street Webster 2B, Room 206 Montreal, Qc., Canada, H3A 2B4 Phone : (514) 398-4965, Fax: 398-8948 Mobile : (514) 712-1768 Office : 527 Av Des Pins O., Room 104 Montreal, Qc., H2W 1S4 From a.janke at gmail.com Tue Dec 8 16:27:57 2009 From: a.janke at gmail.com (Andrew Janke) Date: Wed, 9 Dec 2009 08:27:57 +1100 Subject: [MINC-development] postf problem on grumio [Fwd: RE: help with making pictures of activation] In-Reply-To: References: <4B1EB38A.105@bic.mni.mcgill.ca> Message-ID: Grumio? Is this local execution or remote? I certainly have seen a lot of old BIC GLUT code do strange things and die when you attempt to run it remotely. I would first be looking at the versions of GLUT (well freeglut) on both machines. a On Wed, Dec 9, 2009 at 08:15, Sylvain Milot wrote: > > Hi Mike, > > I tested on 3 systems so far and it segfaults on all 3 - and for both > /usr/local/bic/bin/postf and /usr/local/mni/bin/postf. I also tried with different > data. > > I have CC'ed minc-development but I don't know if this software is actually supported. > > S > > On Tue, 8 Dec 2009, Michael Ferreira wrote: > >> Hello again admins, >> >> I just verified this problem w/ postf myself. ?Basically trying to open any >> Minc image w/ postf on grumio results in a Seg Fault: >> >> grumio: /data/scratch/scratch1/mferre % postf test2.mnc >> Getting image information ... done >> Reading minc data ...................................... done >> Segmentation fault >> >> It works fine on our Linux workstations. >> >> mike >> >> >> >> -------- Original Message -------- >> Subject: RE: help with making pictures of activation >> Date: Sun, 6 Dec 2009 16:32:52 -0500 >> From: Lana Depatie >> To: Michael Ferreira >> >> Hi Mike, >> >> I tried to log in the bic (i.e., login.bic.mni.mcgill.ca) and to type the >> following command in the directory where my file was (cd >> /data/szrisk/szrisk2/lana/icbm_june/anal/as-vgs/adhd-i: "postf >> adhd-i_as-vgs_t.mnc". >> >> I get the following messages: >> "Getting image information .... done" >> "Reading minc data ...done" >> "Segmentation fault" >> and then I get back to the prompt. >> >> Do you know what the problem is? >> Thanks >> > > --- > Sylvain Milot (sylvain at bic.mni.mcgill.ca) > ? ? ? ? ? ? ? (bicadmin at bic.mni.mcgill.ca) > Brain Imaging Centre > Montreal Neurological Institute > 3801 University Street > Webster 2B, Room 206 > Montreal, Qc., Canada, H3A 2B4 > Phone ?: (514) 398-4965, Fax: 398-8948 > Mobile : (514) 712-1768 > Office : 527 Av Des Pins O., Room 104 > ? ? ? ? ?Montreal, Qc., H2W 1S4 > _______________________________________________ > MINC-development mailing list > MINC-development at bic.mni.mcgill.ca > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-development > From sylvain at bic.mni.mcgill.ca Tue Dec 8 17:59:26 2009 From: sylvain at bic.mni.mcgill.ca (Sylvain Milot) Date: Tue, 8 Dec 2009 17:59:26 -0500 (EST) Subject: [MINC-development] postf problem on grumio [Fwd: RE: help with making pictures of activation] In-Reply-To: References: <4B1EB38A.105@bic.mni.mcgill.ca> Message-ID: On Wed, 9 Dec 2009, Andrew Janke wrote: > Grumio? or login ... > Is this local execution or remote? I certainly have seen a lot of old > BIC GLUT code do strange things and die when you attempt to run it > remotely. I would first be looking at the versions of GLUT (well > freeglut) on both machines. both remote and local - although the local system I tested on is lenny 64 bit. it would seem postf works ok locally on 32-bit systems. S > > > a > > On Wed, Dec 9, 2009 at 08:15, Sylvain Milot wrote: >> >> Hi Mike, >> >> I tested on 3 systems so far and it segfaults on all 3 - and for both >> /usr/local/bic/bin/postf and /usr/local/mni/bin/postf. I also tried with different >> data. >> >> I have CC'ed minc-development but I don't know if this software is actually supported. >> >> S >> >> On Tue, 8 Dec 2009, Michael Ferreira wrote: >> >>> Hello again admins, >>> >>> I just verified this problem w/ postf myself. ?Basically trying to open any >>> Minc image w/ postf on grumio results in a Seg Fault: >>> >>> grumio: /data/scratch/scratch1/mferre % postf test2.mnc >>> Getting image information ... done >>> Reading minc data ...................................... done >>> Segmentation fault >>> >>> It works fine on our Linux workstations. >>> >>> mike >>> >>> >>> >>> -------- Original Message -------- >>> Subject: RE: help with making pictures of activation >>> Date: Sun, 6 Dec 2009 16:32:52 -0500 >>> From: Lana Depatie >>> To: Michael Ferreira >>> >>> Hi Mike, >>> >>> I tried to log in the bic (i.e., login.bic.mni.mcgill.ca) and to type the >>> following command in the directory where my file was (cd >>> /data/szrisk/szrisk2/lana/icbm_june/anal/as-vgs/adhd-i: "postf >>> adhd-i_as-vgs_t.mnc". >>> >>> I get the following messages: >>> "Getting image information .... done" >>> "Reading minc data ...done" >>> "Segmentation fault" >>> and then I get back to the prompt. >>> >>> Do you know what the problem is? >>> Thanks >>> >> >> --- >> Sylvain Milot (sylvain at bic.mni.mcgill.ca) >> ? ? ? ? ? ? ? (bicadmin at bic.mni.mcgill.ca) >> Brain Imaging Centre >> Montreal Neurological Institute >> 3801 University Street >> Webster 2B, Room 206 >> Montreal, Qc., Canada, H3A 2B4 >> Phone ?: (514) 398-4965, Fax: 398-8948 >> Mobile : (514) 712-1768 >> Office : 527 Av Des Pins O., Room 104 >> ? ? ? ? ?Montreal, Qc., H2W 1S4 >> _______________________________________________ >> MINC-development mailing list >> MINC-development at bic.mni.mcgill.ca >> http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-development >> > > _______________________________________________ > MINC-development mailing list > MINC-development at bic.mni.mcgill.ca > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-development > --- Sylvain Milot (sylvain at bic.mni.mcgill.ca) (bicadmin at bic.mni.mcgill.ca) Brain Imaging Centre Montreal Neurological Institute 3801 University Street Webster 2B, Room 206 Montreal, Qc., Canada, H3A 2B4 Phone : (514) 398-4965, Fax: 398-8948 Mobile : (514) 712-1768 Office : 527 Av Des Pins O., Room 104 Montreal, Qc., H2W 1S4 From a.janke at gmail.com Tue Dec 8 18:07:49 2009 From: a.janke at gmail.com (Andrew Janke) Date: Wed, 9 Dec 2009 10:07:49 +1100 Subject: [MINC-development] postf problem on grumio [Fwd: RE: help with making pictures of activation] In-Reply-To: References: <4B1EB38A.105@bic.mni.mcgill.ca> Message-ID: > it would seem postf works ok locally on 32-bit systems. Ah, it's the 64 bit short GLUT problem, I thought I fixed this in CVS, where is the version of postf coming from? a From sylvain at bic.mni.mcgill.ca Tue Dec 8 18:15:44 2009 From: sylvain at bic.mni.mcgill.ca (Sylvain Milot) Date: Tue, 8 Dec 2009 18:15:44 -0500 (EST) Subject: [MINC-development] postf problem on grumio [Fwd: RE: help with making pictures of activation] In-Reply-To: References: <4B1EB38A.105@bic.mni.mcgill.ca> Message-ID: On Wed, 9 Dec 2009, Andrew Janke wrote: >> it would seem postf works ok locally on 32-bit systems. > > Ah, it's the 64 bit short GLUT problem, I thought I fixed this in CVS, > where is the version of postf coming from? packages.bic.mni.mcgill.ca/tgz/postf-1.0.02.tar.gz > > > a > _______________________________________________ > MINC-development mailing list > MINC-development at bic.mni.mcgill.ca > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-development > --- Sylvain Milot (sylvain at bic.mni.mcgill.ca) (bicadmin at bic.mni.mcgill.ca) Brain Imaging Centre Montreal Neurological Institute 3801 University Street Webster 2B, Room 206 Montreal, Qc., Canada, H3A 2B4 Phone : (514) 398-4965, Fax: 398-8948 Mobile : (514) 712-1768 Office : 527 Av Des Pins O., Room 104 Montreal, Qc., H2W 1S4 From a.janke at gmail.com Tue Dec 8 18:22:57 2009 From: a.janke at gmail.com (Andrew Janke) Date: Wed, 9 Dec 2009 10:22:57 +1100 Subject: [MINC-development] postf problem on grumio [Fwd: RE: help with making pictures of activation] In-Reply-To: References: <4B1EB38A.105@bic.mni.mcgill.ca> Message-ID: >> Ah, it's the 64 bit short GLUT problem, I thought I fixed this in CVS, >> where is the version of postf coming from? > > packages.bic.mni.mcgill.ca/tgz/postf-1.0.02.tar.gz Try this one that I just dumped there from CVS. http://packages.bic.mni.mcgill.ca/tgz/postf-1.0.03.tar.gz -- Andrew Janke (a.janke at gmail.com || http://a.janke.googlepages.com/) Canberra->Australia +61 (402) 700 883 From sylvain at bic.mni.mcgill.ca Tue Dec 8 19:19:27 2009 From: sylvain at bic.mni.mcgill.ca (Sylvain Milot) Date: Tue, 8 Dec 2009 19:19:27 -0500 (EST) Subject: [MINC-development] postf problem on grumio [Fwd: RE: help with making pictures of activation] In-Reply-To: References: <4B1EB38A.105@bic.mni.mcgill.ca> Message-ID: On Wed, 9 Dec 2009, Andrew Janke wrote: >>> Ah, it's the 64 bit short GLUT problem, I thought I fixed this in CVS, >>> where is the version of postf coming from? >> >> packages.bic.mni.mcgill.ca/tgz/postf-1.0.02.tar.gz > > Try this one that I just dumped there from CVS. > > http://packages.bic.mni.mcgill.ca/tgz/postf-1.0.03.tar.gz thanks - it works. S > > > -- > Andrew Janke > (a.janke at gmail.com || http://a.janke.googlepages.com/) > Canberra->Australia +61 (402) 700 883 > _______________________________________________ > MINC-development mailing list > MINC-development at bic.mni.mcgill.ca > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-development > --- Sylvain Milot (sylvain at bic.mni.mcgill.ca) (bicadmin at bic.mni.mcgill.ca) Brain Imaging Centre Montreal Neurological Institute 3801 University Street Webster 2B, Room 206 Montreal, Qc., Canada, H3A 2B4 Phone : (514) 398-4965, Fax: 398-8948 Mobile : (514) 712-1768 Office : 527 Av Des Pins O., Room 104 Montreal, Qc., H2W 1S4 From mferre at bic.mni.mcgill.ca Wed Dec 9 14:47:16 2009 From: mferre at bic.mni.mcgill.ca (Michael Ferreira) Date: Wed, 09 Dec 2009 14:47:16 -0500 Subject: [MINC-development] postf problem on grumio [Fwd: RE: help with making pictures of activation] In-Reply-To: References: <4B1EB38A.105@bic.mni.mcgill.ca> Message-ID: <4B1FFEC4.7080500@bic.mni.mcgill.ca> Thanks for your help with this Andrew and Sylvain. I built the updated postf on grumio and the resulting executable, when run remotely, loads and displays the image correctly. But if you try to change the colour bar, either with the keyboard (key g,h,or s) or the mouse (colour bar click), the program crashes: X Error of failed request: BadAccess (attempt to access private resource denied) Major opcode of failed request: 88 (X_FreeColors) Serial number of failed request: 4255 Current serial number in output stream: 4256 It's possible that I did not compile this properly. So I was wondering if either of you have tested this colour bar feature yet? Thanks, mike Sylvain Milot wrote: > > On Wed, 9 Dec 2009, Andrew Janke wrote: > >>>> Ah, it's the 64 bit short GLUT problem, I thought I fixed this in CVS, >>>> where is the version of postf coming from? >>> packages.bic.mni.mcgill.ca/tgz/postf-1.0.02.tar.gz >> Try this one that I just dumped there from CVS. >> >> http://packages.bic.mni.mcgill.ca/tgz/postf-1.0.03.tar.gz > > thanks - it works. > > S > >> >> -- >> Andrew Janke >> (a.janke at gmail.com || http://a.janke.googlepages.com/) >> Canberra->Australia +61 (402) 700 883 >> _______________________________________________ >> MINC-development mailing list >> MINC-development at bic.mni.mcgill.ca >> http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-development >> > > --- > Sylvain Milot (sylvain at bic.mni.mcgill.ca) > (bicadmin at bic.mni.mcgill.ca) > Brain Imaging Centre > Montreal Neurological Institute > 3801 University Street > Webster 2B, Room 206 > Montreal, Qc., Canada, H3A 2B4 > Phone : (514) 398-4965, Fax: 398-8948 > Mobile : (514) 712-1768 > Office : 527 Av Des Pins O., Room 104 > Montreal, Qc., H2W 1S4 > _______________________________________________ > MINC-development mailing list > MINC-development at bic.mni.mcgill.ca > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-development From sylvain at bic.mni.mcgill.ca Fri Dec 11 16:21:47 2009 From: sylvain at bic.mni.mcgill.ca (Sylvain Milot) Date: Fri, 11 Dec 2009 16:21:47 -0500 (EST) Subject: [MINC-development] postf problem on grumio [Fwd: RE: help with making pictures of activation] In-Reply-To: <4B1FFEC4.7080500@bic.mni.mcgill.ca> References: <4B1EB38A.105@bic.mni.mcgill.ca> <4B1FFEC4.7080500@bic.mni.mcgill.ca> Message-ID: Just to add to this - this behavior is also present when the program is run locally, for a 64-bit compilation. S On Wed, 9 Dec 2009, Michael Ferreira wrote: > > Thanks for your help with this Andrew and Sylvain. I built the updated > postf on grumio and the resulting executable, when run remotely, loads > and displays the image correctly. > > But if you try to change the colour bar, either with the keyboard (key > g,h,or s) or the mouse (colour bar click), the program crashes: > > X Error of failed request: BadAccess (attempt to access private > resource denied) > Major opcode of failed request: 88 (X_FreeColors) > Serial number of failed request: 4255 > Current serial number in output stream: 4256 > > It's possible that I did not compile this properly. So I was wondering > if either of you have tested this colour bar feature yet? > > > Thanks, > > mike > > > > Sylvain Milot wrote: >> >> On Wed, 9 Dec 2009, Andrew Janke wrote: >> >>>>> Ah, it's the 64 bit short GLUT problem, I thought I fixed this in CVS, >>>>> where is the version of postf coming from? >>>> packages.bic.mni.mcgill.ca/tgz/postf-1.0.02.tar.gz >>> Try this one that I just dumped there from CVS. >>> >>> http://packages.bic.mni.mcgill.ca/tgz/postf-1.0.03.tar.gz >> >> thanks - it works. >> >> S >> >>> >>> -- >>> Andrew Janke >>> (a.janke at gmail.com || http://a.janke.googlepages.com/) >>> Canberra->Australia +61 (402) 700 883 >>> _______________________________________________ >>> MINC-development mailing list >>> MINC-development at bic.mni.mcgill.ca >>> http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-development >>> >> >> --- >> Sylvain Milot (sylvain at bic.mni.mcgill.ca) >> (bicadmin at bic.mni.mcgill.ca) >> Brain Imaging Centre >> Montreal Neurological Institute >> 3801 University Street >> Webster 2B, Room 206 >> Montreal, Qc., Canada, H3A 2B4 >> Phone : (514) 398-4965, Fax: 398-8948 >> Mobile : (514) 712-1768 >> Office : 527 Av Des Pins O., Room 104 >> Montreal, Qc., H2W 1S4 >> _______________________________________________ >> MINC-development mailing list >> MINC-development at bic.mni.mcgill.ca >> http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-development > _______________________________________________ > MINC-development mailing list > MINC-development at bic.mni.mcgill.ca > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-development > --- Sylvain Milot (sylvain at bic.mni.mcgill.ca) (bicadmin at bic.mni.mcgill.ca) Brain Imaging Centre Montreal Neurological Institute 3801 University Street Webster 2B, Room 206 Montreal, Qc., Canada, H3A 2B4 Phone : (514) 398-4965, Fax: 398-8948 Mobile : (514) 712-1768 Office : 527 Av Des Pins O., Room 104 Montreal, Qc., H2W 1S4