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From: Dieter B. <die...@me...> - 2017-05-19 05:14:23
|
Dear colleagues,
I tried to install localrec in scipion (Scipion v1.0.1
(2016-06-30) Augusto) following this instruction:
https://github.com/OPIC-Oxford/localrec/wiki/How-to-install but 'scipion
--help' does not show this software and 'scipion install localrec' does
not find it.
1) how do I install localrec?
2) once installed will it run also by using the latest relion version
(i.e. relion-2.0.x, which I have as a separate and independent install)
or do I have to use the old relion (v-1.4) and if so, can both version
live side by side (for example relion-1.4 within scipion and
relion-2.0.5 outside scipion?
Thanks a lot for hints,
Dieter
------------------------------------------------------------------------
Dieter Blaas,
Max F. Perutz Laboratories
Medical University of Vienna,
Inst. Med. Biochem., Vienna Biocenter (VBC),
Dr. Bohr Gasse 9/3,
A-1030 Vienna, Austria,
Tel: 0043 1 4277 61630,
Fax: 0043 1 4277 9616,
e-mail: die...@me...
------------------------------------------------------------------------
|
|
From: Juha H. <ju...@st...> - 2017-05-17 09:48:23
|
Hi Jose Miguel Thanks, this worked for me. Best wishes, Juha On Wed, May 17, 2017 at 10:55 AM, Jose Miguel de la Rosa Trevin < del...@gm...> wrote: > Hi Veli-Pekka, > > I have found a line that can be causing that LD_LIBRARY_PATH is not > propagated. > > In line 227 of scipion/SConstruct file, a new Environment is created and > it seems that propagating the whole system environment has broken other > compilations. > So, in the next line the PATH is explicitly propagated. > > Could you try to add the following code in line 229: > > env2['ENV']['LD_LIBRARY_PATH'] = env['ENV']['LD_LIBRARY_PATH'] > > > And check if this solves the specific problem you are having. If it does, > then we will need to consider this change > and if it does not affect other systems. > > > Cheers, > Jose Miguel > > > > On Tue, May 16, 2017 at 10:39 PM, Jose Miguel de la Rosa Trevin < > del...@gm...> wrote: > >> Hum, this seems weird. To the best of my knowledge Scons should preserve >> the system LD_LIBRARY_PATH, but it seems that is not working in this way. I >> will take a look at it tomorrow and think in a workaround for you can >> proceed with the installation. >> >> Veli-Pekka, I'm afraid that now you need to compile all the required >> libraries before getting into the Xmipp part. I would like to improve this >> for the future, but we are not there yet. >> >> Bests, >> Jose Miguel >> >> >> On Tue, May 16, 2017 at 10:31 PM, Veli-Pekka Kestilä <vp...@gu...> >> wrote: >> >>> >>> Hi, >>> >>> I checked this and Juha was correct in his theory on missing >>> LD_LIBRARY_PATH. It seems that CSC has changed their environment so that >>> for g++ it's mandatory to have libcloog in LD_LIBRARY_PATH and scipion >>> or scons strips it away from it. >>> >>> If I manually remove libcloog from the LD_LIBRARY_PATH the error also >>> manifested itself in command line. I think the easiest fix for us would >>> be that scipion/scons would respect the system LD_LIBRARY_PATH and would >>> not change it. >>> >>> Is there easy way to skip all the other compilations and just try >>> compile xmipp so that I could check if other compilers provided in the >>> cluster environment would work? >>> >>> Greetings, >>> -vpk >>> >>> On 16.5.2017 16:46, Juha Huiskonen wrote: >>> > Hi Pablo, >>> > >>> > I have these flags: >>> > >>> > CCFLAGS = -std=c99 >>> > CXXFLAGS = >>> > >>> > The missing file is on our system in /appl/opt/cloog/0.18.1/lib/ and >>> > this directory is in my LD_LIBRARY_PATH. >>> > >>> > Is it possible that the LD_LIBRARY_PATH is not carried out to scipion >>> > environment when it tries to compile Xmipp? >>> > >>> > Best wishes, >>> > Juha >>> > >>> > On Tue, May 16, 2017 at 2:34 PM, Pablo Conesa <pc...@cn... >>> > <mailto:pc...@cn...>> wrote: >>> > >>> > Dear all, we don't think we have committed any recent change here >>> > that might has cause the issue. >>> > >>> > Does anyone know which binary requires the missing library? >>> > >>> > And ldd of software/lib/libXmippAlglib.so doesn't seem to depend >>> on it: >>> > >>> > linux-vdso.so.1 => (0x00007ffeefd72000) >>> > libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6 >>> > (0x00007f026fc53000) >>> > libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 >>> (0x00007f026f94a000) >>> > libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 >>> > (0x00007f026f733000) >>> > libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 >>> (0x00007f026f36a000) >>> > /lib64/ld-linux-x86-64.so.2 (0x000055cc2c957000) >>> > >>> > Am I missing (probably since I'm out of my comfort zone here, this >>> > is C++) anything? >>> > >>> > All the best, Pablo. >>> > >>> > >>> > Could you also send what is the content of the below variables at >>> > <SCIPIOn_HOME>/config/scipion.conf ? >>> > >>> > CCFLAGS, CXXFLAGS >>> > >>> > and Does an /echo $CCFLAGS $CXXFLAGS///print something? >>> > >>> > >>> > On 15/05/17 15:35, Juha Huiskonen wrote: >>> >> Hi Jose Miguel, >>> >> >>> >> I am trying to install on the same cluster as Veli-Pekka. I had >>> >> created the directory in March the 13th, but I am not sure if >>> >> that's when I last time successfully installed release-1.1 branch. >>> >> >>> >> Best wishes, >>> >> Juha >>> >> >>> >> On Mon, May 15, 2017 at 2:21 PM, Jose Miguel de la Rosa Trevin >>> >> <del...@gm... <mailto:del...@gm...>> >>> wrote: >>> >> >>> >> Dear Veli-Pekka and Juha, >>> >> >>> >> Thanks for the feedback. Juha, do you remember (approximately) >>> >> when do you successfully installed the branch release-1.1? Is >>> >> you OS also a CentOS distribution? >>> >> >>> >> I have been looking into the logs but none of the recent >>> >> commits looks like causing such error. >>> >> >>> >> Bests, >>> >> Jose Miguel >>> >> >>> >> >>> >> On Mon, May 15, 2017 at 3:14 PM, Juha Huiskonen >>> >> <ju...@st... <mailto:ju...@st...>> wrote: >>> >> >>> >> Hi All, >>> >> >>> >> Just to confirm, I have the same issue as Veli-Pekka >>> >> reported. I had earlier installed release-1.1 >>> >> successfully but now after doing "git pull; scipion >>> >> install" I get an error that it cannot find >>> >> libcloog-isl.so.4. Any ideas? Perhaps this is something >>> >> that the the local sysadmins should install? >>> >> >>> >> Best wishes, >>> >> Juha >>> >> >>> >> On Sun, May 14, 2017 at 10:21 PM, Veli-Pekka Kestilä >>> >> <vp...@gu... <mailto:vp...@gu...>> wrote: >>> >> >>> >> >>> >> Hi, >>> >> >>> >> I am trying to compile Scipion 1.1 for cluster >>> >> (taito.csc.fi <http://taito.csc.fi>) where >>> >> computing nodes are running CentOS 6.9 unfortunately >>> >> compilation fails >>> >> when compiling Xmipp as the alg-library it contains >>> >> needs newer version >>> >> of cloog library than the system has. >>> >> >>> >> I tried to fix the problem by compiling Cloog library >>> >> myself, but this >>> >> didn't work with SCons as it for some reason makes g++ >>> >> to ignore shared >>> >> library infomation. Same compilation on commanline >>> >> works without problem >>> >> >>> >> scons: done reading SConscript files. >>> >> scons: Building targets ... >>> >> g++ -o software/em/xmipp/external/alglib/src/ap.os -c >>> >> -DCLOOG_INT_GMP=1 >>> >> -I/proj/group/taito/scipion-1 >>> .1-fixes/software/include >>> >> -L/proj/group/taito/scipion-1.1-fixes/software/lib >>> >> -L/lib -lcloog-isl >>> >> -lgmp -O3 -fPIC -Isoftware/include >>> >> -Isoftware/em/xmipp/external >>> >> -Isoftware/em/xmipp/libraries -Isoftware/include >>> >> software/em/xmipp/external/alglib/src/ap.cpp >>> >> /homeappl/appl_taito/opt/gcc/ >>> 4.9.3/bin/../libexec/gcc/x86_64-unknown-linux-gnu/4.9.3/cc1plus: >>> >> error while loading shared libraries: >>> >> libcloog-isl.so.4: cannot open >>> >> shared object file: No such file or directory >>> >> scons: *** >>> >> [software/em/xmipp/external/alglib/src/ap.os] Error 1 >>> >> scons: building terminated because of errors. >>> >> >>> >> As as can be seen from the directory listing file is >>> >> in given libpath. >>> >> >>> >> [user@taito-login4 scipion-1.1-fixes]$ ls -la >>> >> /proj/group/taito/scipion-1.1 >>> -fixes/software/lib/libcloo* >>> >> ..../lib/libcloog-isl.a >>> >> ..../lib/libcloog-isl.la <http://libcloog-isl.la> >>> >> ..../lib/libcloog-isl.so -> libcloog-isl.so.4.0.0 >>> >> ..../lib/libcloog-isl.so.4 -> libcloog-isl.so.4.0.0 >>> >> ..../lib/libcloog-isl.so.4.0.0 >>> >> >>> >> I have also tried other ways to give the shared >>> >> library to the Scons but >>> >> they have also failed. Any help on the matter is >>> >> appreciated. >>> >> >>> >> Best Regards, >>> >> Veli-Pekka Kestilä >>> >> >>> >> >>> >> ----------------------------- >>> ------------------------------------------------- >>> >> Check out the vibrant tech community on one of the >>> >> world's most >>> >> engaging tech sites, Slashdot.org! >>> >> http://sdm.link/slashdot >>> >> _______________________________________________ >>> >> scipion-users mailing list >>> >> sci...@li... >>> >> <mailto:sci...@li...> >>> >> https://lists.sourceforge.net >>> /lists/listinfo/scipion-users >>> >> <https://lists.sourceforge.ne >>> t/lists/listinfo/scipion-users> >>> >> >>> >> >>> >> >>> >> ----------------------------- >>> ------------------------------------------------- >>> >> Check out the vibrant tech community on one of the world's >>> >> most >>> >> engaging tech sites, Slashdot.org! >>> http://sdm.link/slashdot >>> >> _______________________________________________ >>> >> scipion-users mailing list >>> >> sci...@li... >>> >> <mailto:sci...@li...> >>> >> https://lists.sourceforge.net >>> /lists/listinfo/scipion-users >>> >> <https://lists.sourceforge.ne >>> t/lists/listinfo/scipion-users> >>> >> >>> >> >>> >> >>> >> >>> >> >>> >> ----------------------------------------------------------- >>> ------------------- >>> >> Check out the vibrant tech community on one of the world's most >>> >> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >>> >> >>> >> >>> >> _______________________________________________ >>> >> scipion-users mailing list >>> >> sci...@li... >>> >> <mailto:sci...@li...> >>> >> https://lists.sourceforge.net/lists/listinfo/scipion-users >>> >> <https://lists.sourceforge.net/lists/listinfo/scipion-users> >>> > >>> > >>> > ----------------------------------------------------------- >>> ------------------- >>> > Check out the vibrant tech community on one of the world's most >>> > engaging tech sites, Slashdot.org! http://sdm.link/slashdot >>> > _______________________________________________ >>> > scipion-users mailing list >>> > sci...@li... >>> > <mailto:sci...@li...> >>> > https://lists.sourceforge.net/lists/listinfo/scipion-users >>> > <https://lists.sourceforge.net/lists/listinfo/scipion-users> >>> > >>> > >>> > >>> > >>> > ------------------------------------------------------------ >>> ------------------ >>> > Check out the vibrant tech community on one of the world's most >>> > engaging tech sites, Slashdot.org! http://sdm.link/slashdot >>> > >>> > >>> > >>> > _______________________________________________ >>> > scipion-users mailing list >>> > sci...@li... >>> > https://lists.sourceforge.net/lists/listinfo/scipion-users >>> > >>> >>> ------------------------------------------------------------ >>> ------------------ >>> Check out the vibrant tech community on one of the world's most >>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >>> _______________________________________________ >>> scipion-users mailing list >>> sci...@li... >>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>> >> >> > > ------------------------------------------------------------ > ------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > |
|
From: Jose M. de la R. T. <del...@gm...> - 2017-05-17 07:55:40
|
Hi Veli-Pekka, I have found a line that can be causing that LD_LIBRARY_PATH is not propagated. In line 227 of scipion/SConstruct file, a new Environment is created and it seems that propagating the whole system environment has broken other compilations. So, in the next line the PATH is explicitly propagated. Could you try to add the following code in line 229: env2['ENV']['LD_LIBRARY_PATH'] = env['ENV']['LD_LIBRARY_PATH'] And check if this solves the specific problem you are having. If it does, then we will need to consider this change and if it does not affect other systems. Cheers, Jose Miguel On Tue, May 16, 2017 at 10:39 PM, Jose Miguel de la Rosa Trevin < del...@gm...> wrote: > Hum, this seems weird. To the best of my knowledge Scons should preserve > the system LD_LIBRARY_PATH, but it seems that is not working in this way. I > will take a look at it tomorrow and think in a workaround for you can > proceed with the installation. > > Veli-Pekka, I'm afraid that now you need to compile all the required > libraries before getting into the Xmipp part. I would like to improve this > for the future, but we are not there yet. > > Bests, > Jose Miguel > > > On Tue, May 16, 2017 at 10:31 PM, Veli-Pekka Kestilä <vp...@gu...> > wrote: > >> >> Hi, >> >> I checked this and Juha was correct in his theory on missing >> LD_LIBRARY_PATH. It seems that CSC has changed their environment so that >> for g++ it's mandatory to have libcloog in LD_LIBRARY_PATH and scipion >> or scons strips it away from it. >> >> If I manually remove libcloog from the LD_LIBRARY_PATH the error also >> manifested itself in command line. I think the easiest fix for us would >> be that scipion/scons would respect the system LD_LIBRARY_PATH and would >> not change it. >> >> Is there easy way to skip all the other compilations and just try >> compile xmipp so that I could check if other compilers provided in the >> cluster environment would work? >> >> Greetings, >> -vpk >> >> On 16.5.2017 16:46, Juha Huiskonen wrote: >> > Hi Pablo, >> > >> > I have these flags: >> > >> > CCFLAGS = -std=c99 >> > CXXFLAGS = >> > >> > The missing file is on our system in /appl/opt/cloog/0.18.1/lib/ and >> > this directory is in my LD_LIBRARY_PATH. >> > >> > Is it possible that the LD_LIBRARY_PATH is not carried out to scipion >> > environment when it tries to compile Xmipp? >> > >> > Best wishes, >> > Juha >> > >> > On Tue, May 16, 2017 at 2:34 PM, Pablo Conesa <pc...@cn... >> > <mailto:pc...@cn...>> wrote: >> > >> > Dear all, we don't think we have committed any recent change here >> > that might has cause the issue. >> > >> > Does anyone know which binary requires the missing library? >> > >> > And ldd of software/lib/libXmippAlglib.so doesn't seem to depend on >> it: >> > >> > linux-vdso.so.1 => (0x00007ffeefd72000) >> > libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6 >> > (0x00007f026fc53000) >> > libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 >> (0x00007f026f94a000) >> > libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 >> > (0x00007f026f733000) >> > libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 >> (0x00007f026f36a000) >> > /lib64/ld-linux-x86-64.so.2 (0x000055cc2c957000) >> > >> > Am I missing (probably since I'm out of my comfort zone here, this >> > is C++) anything? >> > >> > All the best, Pablo. >> > >> > >> > Could you also send what is the content of the below variables at >> > <SCIPIOn_HOME>/config/scipion.conf ? >> > >> > CCFLAGS, CXXFLAGS >> > >> > and Does an /echo $CCFLAGS $CXXFLAGS///print something? >> > >> > >> > On 15/05/17 15:35, Juha Huiskonen wrote: >> >> Hi Jose Miguel, >> >> >> >> I am trying to install on the same cluster as Veli-Pekka. I had >> >> created the directory in March the 13th, but I am not sure if >> >> that's when I last time successfully installed release-1.1 branch. >> >> >> >> Best wishes, >> >> Juha >> >> >> >> On Mon, May 15, 2017 at 2:21 PM, Jose Miguel de la Rosa Trevin >> >> <del...@gm... <mailto:del...@gm...>> >> wrote: >> >> >> >> Dear Veli-Pekka and Juha, >> >> >> >> Thanks for the feedback. Juha, do you remember (approximately) >> >> when do you successfully installed the branch release-1.1? Is >> >> you OS also a CentOS distribution? >> >> >> >> I have been looking into the logs but none of the recent >> >> commits looks like causing such error. >> >> >> >> Bests, >> >> Jose Miguel >> >> >> >> >> >> On Mon, May 15, 2017 at 3:14 PM, Juha Huiskonen >> >> <ju...@st... <mailto:ju...@st...>> wrote: >> >> >> >> Hi All, >> >> >> >> Just to confirm, I have the same issue as Veli-Pekka >> >> reported. I had earlier installed release-1.1 >> >> successfully but now after doing "git pull; scipion >> >> install" I get an error that it cannot find >> >> libcloog-isl.so.4. Any ideas? Perhaps this is something >> >> that the the local sysadmins should install? >> >> >> >> Best wishes, >> >> Juha >> >> >> >> On Sun, May 14, 2017 at 10:21 PM, Veli-Pekka Kestilä >> >> <vp...@gu... <mailto:vp...@gu...>> wrote: >> >> >> >> >> >> Hi, >> >> >> >> I am trying to compile Scipion 1.1 for cluster >> >> (taito.csc.fi <http://taito.csc.fi>) where >> >> computing nodes are running CentOS 6.9 unfortunately >> >> compilation fails >> >> when compiling Xmipp as the alg-library it contains >> >> needs newer version >> >> of cloog library than the system has. >> >> >> >> I tried to fix the problem by compiling Cloog library >> >> myself, but this >> >> didn't work with SCons as it for some reason makes g++ >> >> to ignore shared >> >> library infomation. Same compilation on commanline >> >> works without problem >> >> >> >> scons: done reading SConscript files. >> >> scons: Building targets ... >> >> g++ -o software/em/xmipp/external/alglib/src/ap.os -c >> >> -DCLOOG_INT_GMP=1 >> >> -I/proj/group/taito/scipion-1.1-fixes/software/include >> >> -L/proj/group/taito/scipion-1.1-fixes/software/lib >> >> -L/lib -lcloog-isl >> >> -lgmp -O3 -fPIC -Isoftware/include >> >> -Isoftware/em/xmipp/external >> >> -Isoftware/em/xmipp/libraries -Isoftware/include >> >> software/em/xmipp/external/alglib/src/ap.cpp >> >> /homeappl/appl_taito/opt/gcc/ >> 4.9.3/bin/../libexec/gcc/x86_64-unknown-linux-gnu/4.9.3/cc1plus: >> >> error while loading shared libraries: >> >> libcloog-isl.so.4: cannot open >> >> shared object file: No such file or directory >> >> scons: *** >> >> [software/em/xmipp/external/alglib/src/ap.os] Error 1 >> >> scons: building terminated because of errors. >> >> >> >> As as can be seen from the directory listing file is >> >> in given libpath. >> >> >> >> [user@taito-login4 scipion-1.1-fixes]$ ls -la >> >> /proj/group/taito/scipion-1. >> 1-fixes/software/lib/libcloo* >> >> ..../lib/libcloog-isl.a >> >> ..../lib/libcloog-isl.la <http://libcloog-isl.la> >> >> ..../lib/libcloog-isl.so -> libcloog-isl.so.4.0.0 >> >> ..../lib/libcloog-isl.so.4 -> libcloog-isl.so.4.0.0 >> >> ..../lib/libcloog-isl.so.4.0.0 >> >> >> >> I have also tried other ways to give the shared >> >> library to the Scons but >> >> they have also failed. Any help on the matter is >> >> appreciated. >> >> >> >> Best Regards, >> >> Veli-Pekka Kestilä >> >> >> >> >> >> ----------------------------- >> ------------------------------------------------- >> >> Check out the vibrant tech community on one of the >> >> world's most >> >> engaging tech sites, Slashdot.org! >> >> http://sdm.link/slashdot >> >> _______________________________________________ >> >> scipion-users mailing list >> >> sci...@li... >> >> <mailto:sci...@li...> >> >> https://lists.sourceforge.net/lists/listinfo/scipion- >> users >> >> <https://lists.sourceforge.ne >> t/lists/listinfo/scipion-users> >> >> >> >> >> >> >> >> ----------------------------- >> ------------------------------------------------- >> >> Check out the vibrant tech community on one of the world's >> >> most >> >> engaging tech sites, Slashdot.org! >> http://sdm.link/slashdot >> >> _______________________________________________ >> >> scipion-users mailing list >> >> sci...@li... >> >> <mailto:sci...@li...> >> >> https://lists.sourceforge.net/lists/listinfo/scipion-users >> >> <https://lists.sourceforge.ne >> t/lists/listinfo/scipion-users> >> >> >> >> >> >> >> >> >> >> >> >> ----------------------------------------------------------- >> ------------------- >> >> Check out the vibrant tech community on one of the world's most >> >> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >> >> >> >> >> >> _______________________________________________ >> >> scipion-users mailing list >> >> sci...@li... >> >> <mailto:sci...@li...> >> >> https://lists.sourceforge.net/lists/listinfo/scipion-users >> >> <https://lists.sourceforge.net/lists/listinfo/scipion-users> >> > >> > >> > ----------------------------------------------------------- >> ------------------- >> > Check out the vibrant tech community on one of the world's most >> > engaging tech sites, Slashdot.org! http://sdm.link/slashdot >> > _______________________________________________ >> > scipion-users mailing list >> > sci...@li... >> > <mailto:sci...@li...> >> > https://lists.sourceforge.net/lists/listinfo/scipion-users >> > <https://lists.sourceforge.net/lists/listinfo/scipion-users> >> > >> > >> > >> > >> > ------------------------------------------------------------ >> ------------------ >> > Check out the vibrant tech community on one of the world's most >> > engaging tech sites, Slashdot.org! http://sdm.link/slashdot >> > >> > >> > >> > _______________________________________________ >> > scipion-users mailing list >> > sci...@li... >> > https://lists.sourceforge.net/lists/listinfo/scipion-users >> > >> >> ------------------------------------------------------------ >> ------------------ >> Check out the vibrant tech community on one of the world's most >> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users >> > > |
|
From: Jose M. de la R. T. <del...@gm...> - 2017-05-16 20:39:40
|
Hum, this seems weird. To the best of my knowledge Scons should preserve the system LD_LIBRARY_PATH, but it seems that is not working in this way. I will take a look at it tomorrow and think in a workaround for you can proceed with the installation. Veli-Pekka, I'm afraid that now you need to compile all the required libraries before getting into the Xmipp part. I would like to improve this for the future, but we are not there yet. Bests, Jose Miguel On Tue, May 16, 2017 at 10:31 PM, Veli-Pekka Kestilä <vp...@gu...> wrote: > > Hi, > > I checked this and Juha was correct in his theory on missing > LD_LIBRARY_PATH. It seems that CSC has changed their environment so that > for g++ it's mandatory to have libcloog in LD_LIBRARY_PATH and scipion > or scons strips it away from it. > > If I manually remove libcloog from the LD_LIBRARY_PATH the error also > manifested itself in command line. I think the easiest fix for us would > be that scipion/scons would respect the system LD_LIBRARY_PATH and would > not change it. > > Is there easy way to skip all the other compilations and just try > compile xmipp so that I could check if other compilers provided in the > cluster environment would work? > > Greetings, > -vpk > > On 16.5.2017 16:46, Juha Huiskonen wrote: > > Hi Pablo, > > > > I have these flags: > > > > CCFLAGS = -std=c99 > > CXXFLAGS = > > > > The missing file is on our system in /appl/opt/cloog/0.18.1/lib/ and > > this directory is in my LD_LIBRARY_PATH. > > > > Is it possible that the LD_LIBRARY_PATH is not carried out to scipion > > environment when it tries to compile Xmipp? > > > > Best wishes, > > Juha > > > > On Tue, May 16, 2017 at 2:34 PM, Pablo Conesa <pc...@cn... > > <mailto:pc...@cn...>> wrote: > > > > Dear all, we don't think we have committed any recent change here > > that might has cause the issue. > > > > Does anyone know which binary requires the missing library? > > > > And ldd of software/lib/libXmippAlglib.so doesn't seem to depend on > it: > > > > linux-vdso.so.1 => (0x00007ffeefd72000) > > libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6 > > (0x00007f026fc53000) > > libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 > (0x00007f026f94a000) > > libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 > > (0x00007f026f733000) > > libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 > (0x00007f026f36a000) > > /lib64/ld-linux-x86-64.so.2 (0x000055cc2c957000) > > > > Am I missing (probably since I'm out of my comfort zone here, this > > is C++) anything? > > > > All the best, Pablo. > > > > > > Could you also send what is the content of the below variables at > > <SCIPIOn_HOME>/config/scipion.conf ? > > > > CCFLAGS, CXXFLAGS > > > > and Does an /echo $CCFLAGS $CXXFLAGS///print something? > > > > > > On 15/05/17 15:35, Juha Huiskonen wrote: > >> Hi Jose Miguel, > >> > >> I am trying to install on the same cluster as Veli-Pekka. I had > >> created the directory in March the 13th, but I am not sure if > >> that's when I last time successfully installed release-1.1 branch. > >> > >> Best wishes, > >> Juha > >> > >> On Mon, May 15, 2017 at 2:21 PM, Jose Miguel de la Rosa Trevin > >> <del...@gm... <mailto:del...@gm...>> wrote: > >> > >> Dear Veli-Pekka and Juha, > >> > >> Thanks for the feedback. Juha, do you remember (approximately) > >> when do you successfully installed the branch release-1.1? Is > >> you OS also a CentOS distribution? > >> > >> I have been looking into the logs but none of the recent > >> commits looks like causing such error. > >> > >> Bests, > >> Jose Miguel > >> > >> > >> On Mon, May 15, 2017 at 3:14 PM, Juha Huiskonen > >> <ju...@st... <mailto:ju...@st...>> wrote: > >> > >> Hi All, > >> > >> Just to confirm, I have the same issue as Veli-Pekka > >> reported. I had earlier installed release-1.1 > >> successfully but now after doing "git pull; scipion > >> install" I get an error that it cannot find > >> libcloog-isl.so.4. Any ideas? Perhaps this is something > >> that the the local sysadmins should install? > >> > >> Best wishes, > >> Juha > >> > >> On Sun, May 14, 2017 at 10:21 PM, Veli-Pekka Kestilä > >> <vp...@gu... <mailto:vp...@gu...>> wrote: > >> > >> > >> Hi, > >> > >> I am trying to compile Scipion 1.1 for cluster > >> (taito.csc.fi <http://taito.csc.fi>) where > >> computing nodes are running CentOS 6.9 unfortunately > >> compilation fails > >> when compiling Xmipp as the alg-library it contains > >> needs newer version > >> of cloog library than the system has. > >> > >> I tried to fix the problem by compiling Cloog library > >> myself, but this > >> didn't work with SCons as it for some reason makes g++ > >> to ignore shared > >> library infomation. Same compilation on commanline > >> works without problem > >> > >> scons: done reading SConscript files. > >> scons: Building targets ... > >> g++ -o software/em/xmipp/external/alglib/src/ap.os -c > >> -DCLOOG_INT_GMP=1 > >> -I/proj/group/taito/scipion-1.1-fixes/software/include > >> -L/proj/group/taito/scipion-1.1-fixes/software/lib > >> -L/lib -lcloog-isl > >> -lgmp -O3 -fPIC -Isoftware/include > >> -Isoftware/em/xmipp/external > >> -Isoftware/em/xmipp/libraries -Isoftware/include > >> software/em/xmipp/external/alglib/src/ap.cpp > >> /homeappl/appl_taito/opt/gcc/ > 4.9.3/bin/../libexec/gcc/x86_64-unknown-linux-gnu/4.9.3/cc1plus: > >> error while loading shared libraries: > >> libcloog-isl.so.4: cannot open > >> shared object file: No such file or directory > >> scons: *** > >> [software/em/xmipp/external/alglib/src/ap.os] Error 1 > >> scons: building terminated because of errors. > >> > >> As as can be seen from the directory listing file is > >> in given libpath. > >> > >> [user@taito-login4 scipion-1.1-fixes]$ ls -la > >> /proj/group/taito/scipion-1.1- > fixes/software/lib/libcloo* > >> ..../lib/libcloog-isl.a > >> ..../lib/libcloog-isl.la <http://libcloog-isl.la> > >> ..../lib/libcloog-isl.so -> libcloog-isl.so.4.0.0 > >> ..../lib/libcloog-isl.so.4 -> libcloog-isl.so.4.0.0 > >> ..../lib/libcloog-isl.so.4.0.0 > >> > >> I have also tried other ways to give the shared > >> library to the Scons but > >> they have also failed. Any help on the matter is > >> appreciated. > >> > >> Best Regards, > >> Veli-Pekka Kestilä > >> > >> > >> ------------------------------ > ------------------------------------------------ > >> Check out the vibrant tech community on one of the > >> world's most > >> engaging tech sites, Slashdot.org! > >> http://sdm.link/slashdot > >> _______________________________________________ > >> scipion-users mailing list > >> sci...@li... > >> <mailto:sci...@li...> > >> https://lists.sourceforge.net/ > lists/listinfo/scipion-users > >> <https://lists.sourceforge.net/lists/listinfo/scipion- > users> > >> > >> > >> > >> ------------------------------ > ------------------------------------------------ > >> Check out the vibrant tech community on one of the world's > >> most > >> engaging tech sites, Slashdot.org! http://sdm.link/slashdot > >> _______________________________________________ > >> scipion-users mailing list > >> sci...@li... > >> <mailto:sci...@li...> > >> https://lists.sourceforge.net/lists/listinfo/scipion-users > >> <https://lists.sourceforge.net/lists/listinfo/scipion-users > > > >> > >> > >> > >> > >> > >> ------------------------------------------------------------ > ------------------ > >> Check out the vibrant tech community on one of the world's most > >> engaging tech sites, Slashdot.org! http://sdm.link/slashdot > >> > >> > >> _______________________________________________ > >> scipion-users mailing list > >> sci...@li... > >> <mailto:sci...@li...> > >> https://lists.sourceforge.net/lists/listinfo/scipion-users > >> <https://lists.sourceforge.net/lists/listinfo/scipion-users> > > > > > > ------------------------------------------------------------ > ------------------ > > Check out the vibrant tech community on one of the world's most > > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > > _______________________________________________ > > scipion-users mailing list > > sci...@li... > > <mailto:sci...@li...> > > https://lists.sourceforge.net/lists/listinfo/scipion-users > > <https://lists.sourceforge.net/lists/listinfo/scipion-users> > > > > > > > > > > ------------------------------------------------------------ > ------------------ > > Check out the vibrant tech community on one of the world's most > > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > > > > > > > > _______________________________________________ > > scipion-users mailing list > > sci...@li... > > https://lists.sourceforge.net/lists/listinfo/scipion-users > > > > ------------------------------------------------------------ > ------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
|
From: Veli-Pekka K. <vp...@gu...> - 2017-05-16 20:31:54
|
Hi, I checked this and Juha was correct in his theory on missing LD_LIBRARY_PATH. It seems that CSC has changed their environment so that for g++ it's mandatory to have libcloog in LD_LIBRARY_PATH and scipion or scons strips it away from it. If I manually remove libcloog from the LD_LIBRARY_PATH the error also manifested itself in command line. I think the easiest fix for us would be that scipion/scons would respect the system LD_LIBRARY_PATH and would not change it. Is there easy way to skip all the other compilations and just try compile xmipp so that I could check if other compilers provided in the cluster environment would work? Greetings, -vpk On 16.5.2017 16:46, Juha Huiskonen wrote: > Hi Pablo, > > I have these flags: > > CCFLAGS = -std=c99 > CXXFLAGS = > > The missing file is on our system in /appl/opt/cloog/0.18.1/lib/ and > this directory is in my LD_LIBRARY_PATH. > > Is it possible that the LD_LIBRARY_PATH is not carried out to scipion > environment when it tries to compile Xmipp? > > Best wishes, > Juha > > On Tue, May 16, 2017 at 2:34 PM, Pablo Conesa <pc...@cn... > <mailto:pc...@cn...>> wrote: > > Dear all, we don't think we have committed any recent change here > that might has cause the issue. > > Does anyone know which binary requires the missing library? > > And ldd of software/lib/libXmippAlglib.so doesn't seem to depend on it: > > linux-vdso.so.1 => (0x00007ffeefd72000) > libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6 > (0x00007f026fc53000) > libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f026f94a000) > libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 > (0x00007f026f733000) > libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f026f36a000) > /lib64/ld-linux-x86-64.so.2 (0x000055cc2c957000) > > Am I missing (probably since I'm out of my comfort zone here, this > is C++) anything? > > All the best, Pablo. > > > Could you also send what is the content of the below variables at > <SCIPIOn_HOME>/config/scipion.conf ? > > CCFLAGS, CXXFLAGS > > and Does an /echo $CCFLAGS $CXXFLAGS///print something? > > > On 15/05/17 15:35, Juha Huiskonen wrote: >> Hi Jose Miguel, >> >> I am trying to install on the same cluster as Veli-Pekka. I had >> created the directory in March the 13th, but I am not sure if >> that's when I last time successfully installed release-1.1 branch. >> >> Best wishes, >> Juha >> >> On Mon, May 15, 2017 at 2:21 PM, Jose Miguel de la Rosa Trevin >> <del...@gm... <mailto:del...@gm...>> wrote: >> >> Dear Veli-Pekka and Juha, >> >> Thanks for the feedback. Juha, do you remember (approximately) >> when do you successfully installed the branch release-1.1? Is >> you OS also a CentOS distribution? >> >> I have been looking into the logs but none of the recent >> commits looks like causing such error. >> >> Bests, >> Jose Miguel >> >> >> On Mon, May 15, 2017 at 3:14 PM, Juha Huiskonen >> <ju...@st... <mailto:ju...@st...>> wrote: >> >> Hi All, >> >> Just to confirm, I have the same issue as Veli-Pekka >> reported. I had earlier installed release-1.1 >> successfully but now after doing "git pull; scipion >> install" I get an error that it cannot find >> libcloog-isl.so.4. Any ideas? Perhaps this is something >> that the the local sysadmins should install? >> >> Best wishes, >> Juha >> >> On Sun, May 14, 2017 at 10:21 PM, Veli-Pekka Kestilä >> <vp...@gu... <mailto:vp...@gu...>> wrote: >> >> >> Hi, >> >> I am trying to compile Scipion 1.1 for cluster >> (taito.csc.fi <http://taito.csc.fi>) where >> computing nodes are running CentOS 6.9 unfortunately >> compilation fails >> when compiling Xmipp as the alg-library it contains >> needs newer version >> of cloog library than the system has. >> >> I tried to fix the problem by compiling Cloog library >> myself, but this >> didn't work with SCons as it for some reason makes g++ >> to ignore shared >> library infomation. Same compilation on commanline >> works without problem >> >> scons: done reading SConscript files. >> scons: Building targets ... >> g++ -o software/em/xmipp/external/alglib/src/ap.os -c >> -DCLOOG_INT_GMP=1 >> -I/proj/group/taito/scipion-1.1-fixes/software/include >> -L/proj/group/taito/scipion-1.1-fixes/software/lib >> -L/lib -lcloog-isl >> -lgmp -O3 -fPIC -Isoftware/include >> -Isoftware/em/xmipp/external >> -Isoftware/em/xmipp/libraries -Isoftware/include >> software/em/xmipp/external/alglib/src/ap.cpp >> /homeappl/appl_taito/opt/gcc/4.9.3/bin/../libexec/gcc/x86_64-unknown-linux-gnu/4.9.3/cc1plus: >> error while loading shared libraries: >> libcloog-isl.so.4: cannot open >> shared object file: No such file or directory >> scons: *** >> [software/em/xmipp/external/alglib/src/ap.os] Error 1 >> scons: building terminated because of errors. >> >> As as can be seen from the directory listing file is >> in given libpath. >> >> [user@taito-login4 scipion-1.1-fixes]$ ls -la >> /proj/group/taito/scipion-1.1-fixes/software/lib/libcloo* >> ..../lib/libcloog-isl.a >> ..../lib/libcloog-isl.la <http://libcloog-isl.la> >> ..../lib/libcloog-isl.so -> libcloog-isl.so.4.0.0 >> ..../lib/libcloog-isl.so.4 -> libcloog-isl.so.4.0.0 >> ..../lib/libcloog-isl.so.4.0.0 >> >> I have also tried other ways to give the shared >> library to the Scons but >> they have also failed. Any help on the matter is >> appreciated. >> >> Best Regards, >> Veli-Pekka Kestilä >> >> >> ------------------------------------------------------------------------------ >> Check out the vibrant tech community on one of the >> world's most >> engaging tech sites, Slashdot.org! >> http://sdm.link/slashdot >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> <mailto:sci...@li...> >> https://lists.sourceforge.net/lists/listinfo/scipion-users >> <https://lists.sourceforge.net/lists/listinfo/scipion-users> >> >> >> >> ------------------------------------------------------------------------------ >> Check out the vibrant tech community on one of the world's >> most >> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> <mailto:sci...@li...> >> https://lists.sourceforge.net/lists/listinfo/scipion-users >> <https://lists.sourceforge.net/lists/listinfo/scipion-users> >> >> >> >> >> >> ------------------------------------------------------------------------------ >> Check out the vibrant tech community on one of the world's most >> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >> >> >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> <mailto:sci...@li...> >> https://lists.sourceforge.net/lists/listinfo/scipion-users >> <https://lists.sourceforge.net/lists/listinfo/scipion-users> > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > scipion-users mailing list > sci...@li... > <mailto:sci...@li...> > https://lists.sourceforge.net/lists/listinfo/scipion-users > <https://lists.sourceforge.net/lists/listinfo/scipion-users> > > > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
|
From: Juha H. <ju...@st...> - 2017-05-16 13:47:49
|
Hi Pablo, I have these flags: CCFLAGS = -std=c99 CXXFLAGS = The missing file is on our system in /appl/opt/cloog/0.18.1/lib/ and this directory is in my LD_LIBRARY_PATH. Is it possible that the LD_LIBRARY_PATH is not carried out to scipion environment when it tries to compile Xmipp? Best wishes, Juha On Tue, May 16, 2017 at 2:34 PM, Pablo Conesa <pc...@cn...> wrote: > Dear all, we don't think we have committed any recent change here that > might has cause the issue. > > Does anyone know which binary requires the missing library? > > And ldd of software/lib/libXmippAlglib.so doesn't seem to depend on it: > > linux-vdso.so.1 => (0x00007ffeefd72000) > libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6 > (0x00007f026fc53000) > libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f026f94a000) > libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 > (0x00007f026f733000) > libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f026f36a000) > /lib64/ld-linux-x86-64.so.2 (0x000055cc2c957000) > > Am I missing (probably since I'm out of my comfort zone here, this is C++) > anything? > > All the best, Pablo. > > > Could you also send what is the content of the below variables at > <SCIPIOn_HOME>/config/scipion.conf ? > > CCFLAGS, CXXFLAGS > > and Does an *echo $CCFLAGS $CXXFLAGS* print something? > > On 15/05/17 15:35, Juha Huiskonen wrote: > > Hi Jose Miguel, > > I am trying to install on the same cluster as Veli-Pekka. I had created > the directory in March the 13th, but I am not sure if that's when I last > time successfully installed release-1.1 branch. > > Best wishes, > Juha > > On Mon, May 15, 2017 at 2:21 PM, Jose Miguel de la Rosa Trevin < > del...@gm...> wrote: > >> Dear Veli-Pekka and Juha, >> >> Thanks for the feedback. Juha, do you remember (approximately) when do >> you successfully installed the branch release-1.1? Is you OS also a CentOS >> distribution? >> >> I have been looking into the logs but none of the recent commits looks >> like causing such error. >> >> Bests, >> Jose Miguel >> >> >> On Mon, May 15, 2017 at 3:14 PM, Juha Huiskonen <ju...@st...> >> wrote: >> >>> Hi All, >>> >>> Just to confirm, I have the same issue as Veli-Pekka reported. I had >>> earlier installed release-1.1 successfully but now after doing "git pull; >>> scipion install" I get an error that it cannot find libcloog-isl.so.4. Any >>> ideas? Perhaps this is something that the the local sysadmins should >>> install? >>> >>> Best wishes, >>> Juha >>> >>> On Sun, May 14, 2017 at 10:21 PM, Veli-Pekka Kestilä <vp...@gu...> >>> wrote: >>> >>>> >>>> Hi, >>>> >>>> I am trying to compile Scipion 1.1 for cluster (taito.csc.fi) where >>>> computing nodes are running CentOS 6.9 unfortunately compilation fails >>>> when compiling Xmipp as the alg-library it contains needs newer version >>>> of cloog library than the system has. >>>> >>>> I tried to fix the problem by compiling Cloog library myself, but this >>>> didn't work with SCons as it for some reason makes g++ to ignore shared >>>> library infomation. Same compilation on commanline works without problem >>>> >>>> scons: done reading SConscript files. >>>> scons: Building targets ... >>>> g++ -o software/em/xmipp/external/alglib/src/ap.os -c -DCLOOG_INT_GMP=1 >>>> -I/proj/group/taito/scipion-1.1-fixes/software/include >>>> -L/proj/group/taito/scipion-1.1-fixes/software/lib -L/lib -lcloog-isl >>>> -lgmp -O3 -fPIC -Isoftware/include -Isoftware/em/xmipp/external >>>> -Isoftware/em/xmipp/libraries -Isoftware/include >>>> software/em/xmipp/external/alglib/src/ap.cpp >>>> /homeappl/appl_taito/opt/gcc/4.9.3/bin/../libexec/gcc/x86_64 >>>> -unknown-linux-gnu/4.9.3/cc1plus: >>>> error while loading shared libraries: libcloog-isl.so.4: cannot open >>>> shared object file: No such file or directory >>>> scons: *** [software/em/xmipp/external/alglib/src/ap.os] Error 1 >>>> scons: building terminated because of errors. >>>> >>>> As as can be seen from the directory listing file is in given libpath. >>>> >>>> [user@taito-login4 scipion-1.1-fixes]$ ls -la >>>> /proj/group/taito/scipion-1.1-fixes/software/lib/libcloo* >>>> ..../lib/libcloog-isl.a >>>> ..../lib/libcloog-isl.la >>>> ..../lib/libcloog-isl.so -> libcloog-isl.so.4.0.0 >>>> ..../lib/libcloog-isl.so.4 -> libcloog-isl.so.4.0.0 >>>> ..../lib/libcloog-isl.so.4.0.0 >>>> >>>> I have also tried other ways to give the shared library to the Scons but >>>> they have also failed. Any help on the matter is appreciated. >>>> >>>> Best Regards, >>>> Veli-Pekka Kestilä >>>> >>>> >>>> ------------------------------------------------------------ >>>> ------------------ >>>> Check out the vibrant tech community on one of the world's most >>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >>>> _______________________________________________ >>>> scipion-users mailing list >>>> sci...@li... >>>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>>> >>> >>> >>> ------------------------------------------------------------ >>> ------------------ >>> Check out the vibrant tech community on one of the world's most >>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >>> _______________________________________________ >>> scipion-users mailing list >>> sci...@li... >>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>> >>> >> > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > > > > _______________________________________________ > scipion-users mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/scipion-users > > > > ------------------------------------------------------------ > ------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > |
|
From: Pablo C. <pc...@cn...> - 2017-05-16 11:34:53
|
Dear all, we don't think we have committed any recent change here that
might has cause the issue.
Does anyone know which binary requires the missing library?
And ldd of software/lib/libXmippAlglib.so doesn't seem to depend on it:
linux-vdso.so.1 => (0x00007ffeefd72000)
libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6
(0x00007f026fc53000)
libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f026f94a000)
libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1
(0x00007f026f733000)
libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f026f36a000)
/lib64/ld-linux-x86-64.so.2 (0x000055cc2c957000)
Am I missing (probably since I'm out of my comfort zone here, this is
C++) anything?
All the best, Pablo.
Could you also send what is the content of the below variables at
<SCIPIOn_HOME>/config/scipion.conf ?
CCFLAGS, CXXFLAGS
and Does an /echo $CCFLAGS $CXXFLAGS///print something?
On 15/05/17 15:35, Juha Huiskonen wrote:
> Hi Jose Miguel,
>
> I am trying to install on the same cluster as Veli-Pekka. I had
> created the directory in March the 13th, but I am not sure if that's
> when I last time successfully installed release-1.1 branch.
>
> Best wishes,
> Juha
>
> On Mon, May 15, 2017 at 2:21 PM, Jose Miguel de la Rosa Trevin
> <del...@gm... <mailto:del...@gm...>> wrote:
>
> Dear Veli-Pekka and Juha,
>
> Thanks for the feedback. Juha, do you remember (approximately)
> when do you successfully installed the branch release-1.1? Is you
> OS also a CentOS distribution?
>
> I have been looking into the logs but none of the recent commits
> looks like causing such error.
>
> Bests,
> Jose Miguel
>
>
> On Mon, May 15, 2017 at 3:14 PM, Juha Huiskonen
> <ju...@st... <mailto:ju...@st...>> wrote:
>
> Hi All,
>
> Just to confirm, I have the same issue as Veli-Pekka
> reported. I had earlier installed release-1.1 successfully
> but now after doing "git pull; scipion install" I get an error
> that it cannot find libcloog-isl.so.4. Any ideas? Perhaps this
> is something that the the local sysadmins should install?
>
> Best wishes,
> Juha
>
> On Sun, May 14, 2017 at 10:21 PM, Veli-Pekka Kestilä
> <vp...@gu... <mailto:vp...@gu...>> wrote:
>
>
> Hi,
>
> I am trying to compile Scipion 1.1 for cluster
> (taito.csc.fi <http://taito.csc.fi>) where
> computing nodes are running CentOS 6.9 unfortunately
> compilation fails
> when compiling Xmipp as the alg-library it contains needs
> newer version
> of cloog library than the system has.
>
> I tried to fix the problem by compiling Cloog library
> myself, but this
> didn't work with SCons as it for some reason makes g++ to
> ignore shared
> library infomation. Same compilation on commanline works
> without problem
>
> scons: done reading SConscript files.
> scons: Building targets ...
> g++ -o software/em/xmipp/external/alglib/src/ap.os -c
> -DCLOOG_INT_GMP=1
> -I/proj/group/taito/scipion-1.1-fixes/software/include
> -L/proj/group/taito/scipion-1.1-fixes/software/lib -L/lib
> -lcloog-isl
> -lgmp -O3 -fPIC -Isoftware/include
> -Isoftware/em/xmipp/external
> -Isoftware/em/xmipp/libraries -Isoftware/include
> software/em/xmipp/external/alglib/src/ap.cpp
> /homeappl/appl_taito/opt/gcc/4.9.3/bin/../libexec/gcc/x86_64-unknown-linux-gnu/4.9.3/cc1plus:
> error while loading shared libraries: libcloog-isl.so.4:
> cannot open
> shared object file: No such file or directory
> scons: *** [software/em/xmipp/external/alglib/src/ap.os]
> Error 1
> scons: building terminated because of errors.
>
> As as can be seen from the directory listing file is in
> given libpath.
>
> [user@taito-login4 scipion-1.1-fixes]$ ls -la
> /proj/group/taito/scipion-1.1-fixes/software/lib/libcloo*
> ..../lib/libcloog-isl.a
> ..../lib/libcloog-isl.la <http://libcloog-isl.la>
> ..../lib/libcloog-isl.so -> libcloog-isl.so.4.0.0
> ..../lib/libcloog-isl.so.4 -> libcloog-isl.so.4.0.0
> ..../lib/libcloog-isl.so.4.0.0
>
> I have also tried other ways to give the shared library to
> the Scons but
> they have also failed. Any help on the matter is appreciated.
>
> Best Regards,
> Veli-Pekka Kestilä
>
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's
> most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> <mailto:sci...@li...>
> https://lists.sourceforge.net/lists/listinfo/scipion-users
> <https://lists.sourceforge.net/lists/listinfo/scipion-users>
>
>
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
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> sci...@li...
> <mailto:sci...@li...>
> https://lists.sourceforge.net/lists/listinfo/scipion-users
> <https://lists.sourceforge.net/lists/listinfo/scipion-users>
>
>
>
>
>
> ------------------------------------------------------------------------------
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> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>
>
> _______________________________________________
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> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
|
|
From: Juha H. <ju...@st...> - 2017-05-15 14:09:24
|
Hi Jose Miguel, I am trying to install on the same cluster as Veli-Pekka. I had created the directory in March the 13th, but I am not sure if that's when I last time successfully installed release-1.1 branch. Best wishes, Juha On Mon, May 15, 2017 at 2:21 PM, Jose Miguel de la Rosa Trevin < del...@gm...> wrote: > Dear Veli-Pekka and Juha, > > Thanks for the feedback. Juha, do you remember (approximately) when do you > successfully installed the branch release-1.1? Is you OS also a CentOS > distribution? > > I have been looking into the logs but none of the recent commits looks > like causing such error. > > Bests, > Jose Miguel > > > On Mon, May 15, 2017 at 3:14 PM, Juha Huiskonen <ju...@st...> > wrote: > >> Hi All, >> >> Just to confirm, I have the same issue as Veli-Pekka reported. I had >> earlier installed release-1.1 successfully but now after doing "git pull; >> scipion install" I get an error that it cannot find libcloog-isl.so.4. Any >> ideas? Perhaps this is something that the the local sysadmins should >> install? >> >> Best wishes, >> Juha >> >> On Sun, May 14, 2017 at 10:21 PM, Veli-Pekka Kestilä <vp...@gu...> >> wrote: >> >>> >>> Hi, >>> >>> I am trying to compile Scipion 1.1 for cluster (taito.csc.fi) where >>> computing nodes are running CentOS 6.9 unfortunately compilation fails >>> when compiling Xmipp as the alg-library it contains needs newer version >>> of cloog library than the system has. >>> >>> I tried to fix the problem by compiling Cloog library myself, but this >>> didn't work with SCons as it for some reason makes g++ to ignore shared >>> library infomation. Same compilation on commanline works without problem >>> >>> scons: done reading SConscript files. >>> scons: Building targets ... >>> g++ -o software/em/xmipp/external/alglib/src/ap.os -c -DCLOOG_INT_GMP=1 >>> -I/proj/group/taito/scipion-1.1-fixes/software/include >>> -L/proj/group/taito/scipion-1.1-fixes/software/lib -L/lib -lcloog-isl >>> -lgmp -O3 -fPIC -Isoftware/include -Isoftware/em/xmipp/external >>> -Isoftware/em/xmipp/libraries -Isoftware/include >>> software/em/xmipp/external/alglib/src/ap.cpp >>> /homeappl/appl_taito/opt/gcc/4.9.3/bin/../libexec/gcc/x86_64 >>> -unknown-linux-gnu/4.9.3/cc1plus: >>> error while loading shared libraries: libcloog-isl.so.4: cannot open >>> shared object file: No such file or directory >>> scons: *** [software/em/xmipp/external/alglib/src/ap.os] Error 1 >>> scons: building terminated because of errors. >>> >>> As as can be seen from the directory listing file is in given libpath. >>> >>> [user@taito-login4 scipion-1.1-fixes]$ ls -la >>> /proj/group/taito/scipion-1.1-fixes/software/lib/libcloo* >>> ..../lib/libcloog-isl.a >>> ..../lib/libcloog-isl.la >>> ..../lib/libcloog-isl.so -> libcloog-isl.so.4.0.0 >>> ..../lib/libcloog-isl.so.4 -> libcloog-isl.so.4.0.0 >>> ..../lib/libcloog-isl.so.4.0.0 >>> >>> I have also tried other ways to give the shared library to the Scons but >>> they have also failed. Any help on the matter is appreciated. >>> >>> Best Regards, >>> Veli-Pekka Kestilä >>> >>> >>> ------------------------------------------------------------ >>> ------------------ >>> Check out the vibrant tech community on one of the world's most >>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >>> _______________________________________________ >>> scipion-users mailing list >>> sci...@li... >>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>> >> >> >> ------------------------------------------------------------ >> ------------------ >> Check out the vibrant tech community on one of the world's most >> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users >> >> > |
|
From: Jose M. de la R. T. <del...@gm...> - 2017-05-15 13:21:53
|
Dear Veli-Pekka and Juha, Thanks for the feedback. Juha, do you remember (approximately) when do you successfully installed the branch release-1.1? Is you OS also a CentOS distribution? I have been looking into the logs but none of the recent commits looks like causing such error. Bests, Jose Miguel On Mon, May 15, 2017 at 3:14 PM, Juha Huiskonen <ju...@st...> wrote: > Hi All, > > Just to confirm, I have the same issue as Veli-Pekka reported. I had > earlier installed release-1.1 successfully but now after doing "git pull; > scipion install" I get an error that it cannot find libcloog-isl.so.4. Any > ideas? Perhaps this is something that the the local sysadmins should > install? > > Best wishes, > Juha > > On Sun, May 14, 2017 at 10:21 PM, Veli-Pekka Kestilä <vp...@gu...> > wrote: > >> >> Hi, >> >> I am trying to compile Scipion 1.1 for cluster (taito.csc.fi) where >> computing nodes are running CentOS 6.9 unfortunately compilation fails >> when compiling Xmipp as the alg-library it contains needs newer version >> of cloog library than the system has. >> >> I tried to fix the problem by compiling Cloog library myself, but this >> didn't work with SCons as it for some reason makes g++ to ignore shared >> library infomation. Same compilation on commanline works without problem >> >> scons: done reading SConscript files. >> scons: Building targets ... >> g++ -o software/em/xmipp/external/alglib/src/ap.os -c -DCLOOG_INT_GMP=1 >> -I/proj/group/taito/scipion-1.1-fixes/software/include >> -L/proj/group/taito/scipion-1.1-fixes/software/lib -L/lib -lcloog-isl >> -lgmp -O3 -fPIC -Isoftware/include -Isoftware/em/xmipp/external >> -Isoftware/em/xmipp/libraries -Isoftware/include >> software/em/xmipp/external/alglib/src/ap.cpp >> /homeappl/appl_taito/opt/gcc/4.9.3/bin/../libexec/gcc/x86_64 >> -unknown-linux-gnu/4.9.3/cc1plus: >> error while loading shared libraries: libcloog-isl.so.4: cannot open >> shared object file: No such file or directory >> scons: *** [software/em/xmipp/external/alglib/src/ap.os] Error 1 >> scons: building terminated because of errors. >> >> As as can be seen from the directory listing file is in given libpath. >> >> [user@taito-login4 scipion-1.1-fixes]$ ls -la >> /proj/group/taito/scipion-1.1-fixes/software/lib/libcloo* >> ..../lib/libcloog-isl.a >> ..../lib/libcloog-isl.la >> ..../lib/libcloog-isl.so -> libcloog-isl.so.4.0.0 >> ..../lib/libcloog-isl.so.4 -> libcloog-isl.so.4.0.0 >> ..../lib/libcloog-isl.so.4.0.0 >> >> I have also tried other ways to give the shared library to the Scons but >> they have also failed. Any help on the matter is appreciated. >> >> Best Regards, >> Veli-Pekka Kestilä >> >> >> ------------------------------------------------------------ >> ------------------ >> Check out the vibrant tech community on one of the world's most >> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users >> > > > ------------------------------------------------------------ > ------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > |
|
From: Juha H. <ju...@st...> - 2017-05-15 13:15:20
|
Hi All, Just to confirm, I have the same issue as Veli-Pekka reported. I had earlier installed release-1.1 successfully but now after doing "git pull; scipion install" I get an error that it cannot find libcloog-isl.so.4. Any ideas? Perhaps this is something that the the local sysadmins should install? Best wishes, Juha On Sun, May 14, 2017 at 10:21 PM, Veli-Pekka Kestilä <vp...@gu...> wrote: > > Hi, > > I am trying to compile Scipion 1.1 for cluster (taito.csc.fi) where > computing nodes are running CentOS 6.9 unfortunately compilation fails > when compiling Xmipp as the alg-library it contains needs newer version > of cloog library than the system has. > > I tried to fix the problem by compiling Cloog library myself, but this > didn't work with SCons as it for some reason makes g++ to ignore shared > library infomation. Same compilation on commanline works without problem > > scons: done reading SConscript files. > scons: Building targets ... > g++ -o software/em/xmipp/external/alglib/src/ap.os -c -DCLOOG_INT_GMP=1 > -I/proj/group/taito/scipion-1.1-fixes/software/include > -L/proj/group/taito/scipion-1.1-fixes/software/lib -L/lib -lcloog-isl > -lgmp -O3 -fPIC -Isoftware/include -Isoftware/em/xmipp/external > -Isoftware/em/xmipp/libraries -Isoftware/include > software/em/xmipp/external/alglib/src/ap.cpp > /homeappl/appl_taito/opt/gcc/4.9.3/bin/../libexec/gcc/x86_ > 64-unknown-linux-gnu/4.9.3/cc1plus: > error while loading shared libraries: libcloog-isl.so.4: cannot open > shared object file: No such file or directory > scons: *** [software/em/xmipp/external/alglib/src/ap.os] Error 1 > scons: building terminated because of errors. > > As as can be seen from the directory listing file is in given libpath. > > [user@taito-login4 scipion-1.1-fixes]$ ls -la > /proj/group/taito/scipion-1.1-fixes/software/lib/libcloo* > ..../lib/libcloog-isl.a > ..../lib/libcloog-isl.la > ..../lib/libcloog-isl.so -> libcloog-isl.so.4.0.0 > ..../lib/libcloog-isl.so.4 -> libcloog-isl.so.4.0.0 > ..../lib/libcloog-isl.so.4.0.0 > > I have also tried other ways to give the shared library to the Scons but > they have also failed. Any help on the matter is appreciated. > > Best Regards, > Veli-Pekka Kestilä > > > ------------------------------------------------------------ > ------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
|
From: Veli-Pekka K. <vp...@gu...> - 2017-05-14 21:38:24
|
Hi, I am trying to compile Scipion 1.1 for cluster (taito.csc.fi) where computing nodes are running CentOS 6.9 unfortunately compilation fails when compiling Xmipp as the alg-library it contains needs newer version of cloog library than the system has. I tried to fix the problem by compiling Cloog library myself, but this didn't work with SCons as it for some reason makes g++ to ignore shared library infomation. Same compilation on commanline works without problem scons: done reading SConscript files. scons: Building targets ... g++ -o software/em/xmipp/external/alglib/src/ap.os -c -DCLOOG_INT_GMP=1 -I/proj/group/taito/scipion-1.1-fixes/software/include -L/proj/group/taito/scipion-1.1-fixes/software/lib -L/lib -lcloog-isl -lgmp -O3 -fPIC -Isoftware/include -Isoftware/em/xmipp/external -Isoftware/em/xmipp/libraries -Isoftware/include software/em/xmipp/external/alglib/src/ap.cpp /homeappl/appl_taito/opt/gcc/4.9.3/bin/../libexec/gcc/x86_64-unknown-linux-gnu/4.9.3/cc1plus: error while loading shared libraries: libcloog-isl.so.4: cannot open shared object file: No such file or directory scons: *** [software/em/xmipp/external/alglib/src/ap.os] Error 1 scons: building terminated because of errors. As as can be seen from the directory listing file is in given libpath. [user@taito-login4 scipion-1.1-fixes]$ ls -la /proj/group/taito/scipion-1.1-fixes/software/lib/libcloo* ..../lib/libcloog-isl.a ..../lib/libcloog-isl.la ..../lib/libcloog-isl.so -> libcloog-isl.so.4.0.0 ..../lib/libcloog-isl.so.4 -> libcloog-isl.so.4.0.0 ..../lib/libcloog-isl.so.4.0.0 I have also tried other ways to give the shared library to the Scons but they have also failed. Any help on the matter is appreciated. Best Regards, Veli-Pekka Kestilä |
|
From: Dmitry S. <sem...@gm...> - 2017-05-14 10:01:45
|
Dear colleagues, The protocol *xmipp3 - movie extract* ends up with the following error STARTED: processMovieStep, step 1 00012: 2017-05-14 10:42:24.500805 00013: Processing movie: Runs/028262_XmippProtExtractMovieParticles/tmp/movie_000001/FoilHole_26594250_Data_25564800_25564801_20160826_2007-21923.mrc 00014: Traceback (most recent call last): 00015: File "/software/software/Scipion/1.1_2017-02-06-foss-2016a/pyworkflow/protocol/protocol.py", line 182, in run 00016: self._run() 00017: File "/software/software/Scipion/1.1_2017-02-06-foss-2016a/pyworkflow/protocol/protocol.py", line 228, in _run 00018: resultFiles = self._runFunc() 00019: File "/software/software/Scipion/1.1_2017-02-06-foss-2016a/pyworkflow/protocol/protocol.py", line 224, in _runFunc 00020: return self._func(*self._args) 00021: File "/software/software/Scipion/1.1_2017-02-06-foss-2016a/pyworkflow/em/protocol/protocol_movies.py", line 267, in processMovieStep 00022: self._processMovie(movie) 00023: File "/software/software/Scipion/1.1_2017-02-06-foss-2016a/pyworkflow/em/packages/xmipp3/protocol_extract_particles_movies.py", line 191, in _processMovie 00024: x, y, n = movie.getDim() 00025: TypeError: 'NoneType' object is not iterable 00026: Protocol failed: 'NoneType' object is not iterable 00027: FAILED: processMovieStep, step 1 00028: 2017-05-14 10:42:25.035791 00029: ------------------- PROTOCOL FAILED (DONE 1/5141) ```````````````````````````````````````````````````````````````````````````````````````````````````````````````````````````````````` 00001: 2017-05-14 10:42:18,291 INFO: RUNNING PROTOCOL ----------------- 00002: 2017-05-14 10:42:18,292 INFO: PID: 58347 00003: 2017-05-14 10:42:18,292 INFO: Scipion: v1.1-beta (2017-04-21) Balbino 00004: 2017-05-14 10:42:18,292 INFO: currentDir: /scratch/p260888/ScipionUserData/projects/tetra_parts_ 00005: 2017-05-14 10:42:18,293 INFO: workingDir: Runs/028262_XmippProtExtractMovieParticles 00006: 2017-05-14 10:42:18,293 INFO: runMode: Restart 00007: 2017-05-14 10:42:18,293 INFO: MPI: 1 00008: 2017-05-14 10:42:18,293 INFO: threads: 1 00009: 2017-05-14 10:42:22,697 INFO: Starting at step: 1 00010: 2017-05-14 10:42:24,443 INFO: Running steps 00011: 2017-05-14 10:42:24,500 INFO: STARTED: processMovieStep, step 1 00012: 2017-05-14 10:42:24,501 INFO: 2017-05-14 10:42:24.500805 00013: 2017-05-14 10:42:25,034 INFO: Processing movie: Runs/028262_XmippProtExtractMovieParticles/tmp/movie_000001/FoilHole_26594250_Data_25564800_25564801_20160826_2007-21923.mrc 00014: 2017-05-14 10:42:25,037 ERROR: Protocol failed: 'NoneType' object is not iterable 00015: 2017-05-14 10:42:25,126 INFO: FAILED: processMovieStep, step 1 00016: 2017-05-14 10:42:25,126 INFO: 2017-05-14 10:42:25.035791 00017: 2017-05-14 10:42:25,308 INFO: ------------------- PROTOCOL FAILED (DONE 1/5141) 00018: 2017-05-14 10:42:29,073 INFO: ------------------- PROTOCOL FAILED (DONE 1/5141) Any ideas how to fix that? Thank you Sincerely, Dmitry Scipion v1.1-beta (2017-04-21) Balbino |
|
From: Dieter B. <die...@me...> - 2017-05-13 05:45:36
|
Hi,
I have now explored the problem further:
I can display the class_avages with xmipp_showJ by using either the
metadata file or the image stack but when running the command below I
always get the error (bold)
Input metadata : carenumbered.xmd
Output rootname : rec_random
T0 : 0.1
Number of random iterations : 10
Number of greedy iterations : 0
Rejection percentage : 25
Number of threads : 1
Apply positive constraint : 1
Keep intermediate volumes : 0
Angular sampling : 5
Symmetry for projections : I2
*XMIPP_ERROR 52: Parameter incorrect.**
**ImageBase::openFile Cannot open an empty Filename.**
**File: libraries/data/xmipp_image_base.cpp line: 493*
So, which filename is empty?
thanks a lot for hints, Dieter
------------------------------------------------------------------------
Dieter Blaas,
Max F. Perutz Laboratories
Medical University of Vienna,
Inst. Med. Biochem., Vienna Biocenter (VBC),
Dr. Bohr Gasse 9/3,
A-1030 Vienna, Austria,
Tel: 0043 1 4277 61630,
Fax: 0043 1 4277 9616,
e-mail: die...@me...
------------------------------------------------------------------------
Am 12.05.2017 um 22:56 schrieb Grigory Sharov:
> Hello Dieter,
>
> you could try running the command:
>
> scipion run
> $YOUR_SCIPION_HOME/software/em/xmipp/bin/xmipp_volume_initial_simulated_annealing
> --gui
>
> Best regards,
> Grigory
>
> --------------------------------------------------------------------------------
> Grigory Sharov, Ph.D.
>
> MRC Laboratory of Molecular Biology,
> Francis Crick Avenue,
> Cambridge Biomedical Campus,
> Cambridge CB2 0QH, UK.
> tel. +44 (0) 1223 267542 <tel:+44%201223%20267542>
> e-mail: gs...@mr... <mailto:gs...@mr...>
>
> On Fri, May 12, 2017 at 9:50 PM, Dieter Blaas
> <die...@me... <mailto:die...@me...>>
> wrote:
>
> Hi Roberto,
>
> I wanted to use simulated annealing from an apparently correct scipion
> installation (no errors issued during compilation and configure) but
> when I run either:
>
> scipion xmipp_volume_initial_simulated_annealing --gui
>
> or:
>
> xmipp_volume_initial_simulated_annealing --gui
>
> I always get:
>
> /usr/bin/env: xmipp_python: No such file or directory
>
> Should xmipp_python not be installed automatically? It is not in
> ../xmipp/bin/ where it was in the older versions and I can neither
> find
> it anywhere else!
>
> Thanks for hints, best wishes, Dieter
>
> ------------------------------------------------------------------------
> Dieter Blaas,
> Max F. Perutz Laboratories
> Medical University of Vienna,
> Inst. Med. Biochem., Vienna Biocenter (VBC),
> Dr. Bohr Gasse 9/3,
> A-1030 Vienna, Austria,
> Tel: 0043 1 4277 61630 <tel:0043%201%204277%2061630>,
> Fax: 0043 1 4277 9616 <tel:0043%201%204277%209616>,
> e-mail: die...@me...
> <mailto:die...@me...>
> ------------------------------------------------------------------------
>
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> Newxmipp-users mailing list
> New...@li...
> <mailto:New...@li...>
> https://lists.sourceforge.net/lists/listinfo/newxmipp-users
> <https://lists.sourceforge.net/lists/listinfo/newxmipp-users>
>
>
|
|
From: Grigory S. <sha...@gm...> - 2017-05-12 20:56:44
|
Hello Dieter, you could try running the command: scipion run $YOUR_SCIPION_HOME/software/em/xmipp/bin/xmipp_volume_initial_simulated_annealing --gui Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. tel. +44 (0) 1223 267542 <+44%201223%20267542> e-mail: gs...@mr... On Fri, May 12, 2017 at 9:50 PM, Dieter Blaas <die...@me... > wrote: > Hi Roberto, > > I wanted to use simulated annealing from an apparently correct scipion > installation (no errors issued during compilation and configure) but > when I run either: > > scipion xmipp_volume_initial_simulated_annealing --gui > > or: > > xmipp_volume_initial_simulated_annealing --gui > > I always get: > > /usr/bin/env: xmipp_python: No such file or directory > > Should xmipp_python not be installed automatically? It is not in > ../xmipp/bin/ where it was in the older versions and I can neither find > it anywhere else! > > Thanks for hints, best wishes, Dieter > > ------------------------------------------------------------------------ > Dieter Blaas, > Max F. Perutz Laboratories > Medical University of Vienna, > Inst. Med. Biochem., Vienna Biocenter (VBC), > Dr. Bohr Gasse 9/3, > A-1030 Vienna, Austria, > Tel: 0043 1 4277 61630, > Fax: 0043 1 4277 9616, > e-mail: die...@me... > ------------------------------------------------------------------------ > > > ------------------------------------------------------------ > ------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > Newxmipp-users mailing list > New...@li... > https://lists.sourceforge.net/lists/listinfo/newxmipp-users > |
|
From: Pablo C. <pc...@cn...> - 2017-05-12 17:06:15
|
HI Dmitry, I've just used it and is working fine here with the same version. Could you please send the complete log to see if there is something weird? Also, how does the cft input looks like? Thans for asking, Pablo. On 12/05/17 18:47, Dmitry Semchonok wrote: > Dear colleagues - > > additions about xmipp3 - extract particles > > > When I don't use the CTF file the protocol seems to work > > Sincerely, > Dmitry > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users |
|
From: Dmitry S. <sem...@gm...> - 2017-05-12 16:48:03
|
Dear colleagues - additions about xmipp3 - extract particles When I don't use the CTF file the protocol seems to work Sincerely, Dmitry |
|
From: Dmitry S. <sem...@gm...> - 2017-05-12 16:41:52
|
Dear colleagues, During extraction, I got the following error: *Protocol failed: Command 'xmipp_micrograph_scissor -i Runs/001958_XmippProtExtractParticles/tmp/10_noDust.xmp --pos particles@Runs/001958_XmippProtExtractParticles/extra/10.pos -o Runs/001958_XmippProtExtractParticles/extra/10 --Xdim 160 --ctfparam Runs/001958_XmippProtExtractParticles/tmp/10.ctfParam' returned non-zero exit status 22* The Scipion version *Scipion v1.1-beta (2017-04-21) Balbino* Could you please help? Sincerely, Dmitry |
|
From: Jose M. de la R. T. <del...@gm...> - 2017-05-03 16:06:23
|
Hi Chris, What version of Scipion are you trying to run? I would recommend to use the 'release-1.1' branch from GitHub that will be the next stable release. The error you show seems to be that CL2D program need to use more than one MPI processes, try to use 2 or higher. I think that in the new version this is validated and made more clear to the user. Bests, Jose Miguel On Wed, May 3, 2017 at 5:47 PM, Christopher Arthur <cpa...@gm...> wrote: > Hi, > I am attempting to install Scipion on Ubuntu and running into the > following errors when running Xmipp 2d align > > [image: Inline image 1] > > Any assistance is appreciated. > best, > Chris > > > ------------------------------------------------------------ > ------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > |
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From: Christopher A. <cpa...@gm...> - 2017-05-03 15:48:02
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Hi, I am attempting to install Scipion on Ubuntu and running into the following errors when running Xmipp 2d align [image: Inline image 1] Any assistance is appreciated. best, Chris |
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From: Dmitry S. <sem...@gm...> - 2017-05-02 10:19:16
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Dear colleagues, Small question just for clear understanding - with relion-postprocessing we are obtaining the several maps: *postprocess.mrc* *postprocess_automask.mrc* *postprocess_masked.mrc* I would like to know the difference(mask..auto....) and which one we use as a final? What is your understanding? Thank you! Sincerely, Dmitry |
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From: Carlos O. S. <co...@cn...> - 2017-05-02 07:36:55
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On 04/29/17 11:35, Dmitry Semchonok wrote: > Dear colleagues, > > > > 2. xmipp3 - correlation alignment / optical alignment > > > > > 2.1 correlation alignment > > - from time to time the protocol stops. When I resubmit it continues > working. > But the question is why does that happen: problem with my dataset > and/or bug? > Without a specific error, it is hard to say. > > 2.2 optical alignment > > - if you may remember the problem was that it finished because of an > error in 1 file. > > Is there already the solution for skipping the movies that causing the > error? > Yes, we have on our roof to make the protocol more robust to incorrect movies. > Alternatively, I removed that file (it looked fine in terms of frames > and visibility - I can send it for the analysis) and have to rerun the > xmipp3-correlation again. But there is no guarantee that the program > will not stop on some other file. > Kind regards, Carlos Oscar -- ------------------------------------------------------------------------ Carlos Oscar Sánchez Sorzano e-mail: co...@cn... Biocomputing unit http://biocomp.cnb.csic.es National Center of Biotechnology (CSIC) c/Darwin, 3 Campus Universidad Autónoma (Cantoblanco) Tlf: 34-91-585 4510 28049 MADRID (SPAIN) Fax: 34-91-585 4506 ------------------------------------------------------------------------ |
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From: Carlos O. S. <co...@cn...> - 2017-05-02 07:34:18
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Dear all, On 04/29/17 17:05, Grigory Sharov wrote: > Hi Dmitry, > > I can try to answer a couple of your questions: > > I assume you are in release-1.1 branch (Scipion v1.1-beta (2017-04-21) > Balbino)? > > 1) I think it's a bad idea to use aligned movies as input for a second > alignment - the interpolation will cause you more problems and will > not improve any alignment. Also, motioncor2 cannot read input shifts > for the movies. If I'm right, Scipion is not producing an interpolated output movie, unless the corresponding option is activated. The default behavior is to attach shift parameters to each frame, so that the next protocol can align the frames properly. I don't know the details, but I tend to agree with Grigori in that motioncor2 cannot read the shifts. It makes sense to correct for global shifts (motioncorr or xmipp correlation) and then for local shifts with optical flow. As far as I understand motioncorr2 cannot produce aligned frames, and I would also be suspicious of the double interpolation (the one done by motioncorr2 and the one by optical flow). I find less useful a double correction by global shifts. Kind regards, Carlos Oscar > > 3) hm, can't seem to reproduce your error (neither in normal, no in > streaming mode). Is it failing in the middle of the run (not first few > movies)? > > Best regards, > Grigory > > -------------------------------------------------------------------------------- > Grigory Sharov, Ph.D. > > MRC Laboratory of Molecular Biology, > Francis Crick Avenue, > Cambridge Biomedical Campus, > Cambridge CB2 0QH, UK. > tel. +44 (0) 1223 267542 <tel:+44%201223%20267542> > e-mail: gs...@mr... <mailto:gs...@mr...> > > On Sat, Apr 29, 2017 at 10:35 AM, Dmitry Semchonok > <sem...@gm... <mailto:sem...@gm...>> wrote: > > Dear colleagues, > > The issue is again with movie correction scripts. > > 1. Motioncorr2 > As input, I use the movie stacks (can I use corrected movies as an > input to increase the quality - for example after > xmipp3-correlation alignment or it will be repetition?) and get > the error - > > ProgrammingError: Incorrect number of bindings supplied. The > current statement uses 32, and there are 22 supplied. > (the git was updated) > > Встроенное изображение 1 > > How can I fix that? > > > 2. xmipp3 - correlation alignment / optical alignment > > > > > 2.1 correlation alignment > > - from time to time the protocol stops. When I resubmit it > continues working. > But the question is why does that happen: problem with my dataset > and/or bug? > > > 2.2 optical alignment > > - if you may remember the problem was that it finished because of > an error in 1 file. > > Is there already the solution for skipping the movies that causing > the error? > > Alternatively, I removed that file (it looked fine in terms of > frames and visibility - I can send it for the analysis) and have > to rerun the xmipp3-correlation again. But there is no guarantee > that the program will not stop on some other file. > > > > 3. grigoriefflab - Input - movie stacks > > stops in the beginning with error - > > Input stack filename > 14274: > [Runs/022622_ProtUnblur/tmp/movie_000010/FoilHole_26594251_Data_25564934_25564935_20160826_2014-21929.mrc] > : 24 > 14275: > 14276: No Such File - please enter a valid filename > > > > > Встроенное изображение 2 > > > > Sincerely, > Dmitry > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > scipion-users mailing list > sci...@li... > <mailto:sci...@li...> > https://lists.sourceforge.net/lists/listinfo/scipion-users > <https://lists.sourceforge.net/lists/listinfo/scipion-users> > > > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users -- ------------------------------------------------------------------------ Carlos Oscar Sánchez Sorzano e-mail: co...@cn... Biocomputing unit http://biocomp.cnb.csic.es National Center of Biotechnology (CSIC) c/Darwin, 3 Campus Universidad Autónoma (Cantoblanco) Tlf: 34-91-585 4510 28049 MADRID (SPAIN) Fax: 34-91-585 4506 ------------------------------------------------------------------------ |
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From: Grigory S. <sha...@gm...> - 2017-04-29 15:05:50
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Hi Dmitry, I can try to answer a couple of your questions: I assume you are in release-1.1 branch (Scipion v1.1-beta (2017-04-21) Balbino)? 1) I think it's a bad idea to use aligned movies as input for a second alignment - the interpolation will cause you more problems and will not improve any alignment. Also, motioncor2 cannot read input shifts for the movies. 3) hm, can't seem to reproduce your error (neither in normal, no in streaming mode). Is it failing in the middle of the run (not first few movies)? Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. tel. +44 (0) 1223 267542 <+44%201223%20267542> e-mail: gs...@mr... On Sat, Apr 29, 2017 at 10:35 AM, Dmitry Semchonok <sem...@gm...> wrote: > Dear colleagues, > > The issue is again with movie correction scripts. > > 1. Motioncorr2 > As input, I use the movie stacks (can I use corrected movies as an input > to increase the quality - for example after xmipp3-correlation alignment or > it will be repetition?) and get the error - > > ProgrammingError: Incorrect number of bindings supplied. The current > statement uses 32, and there are 22 supplied. > (the git was updated) > > [image: Встроенное изображение 1] > > How can I fix that? > > > 2. xmipp3 - correlation alignment / optical alignment > > > > > 2.1 correlation alignment > > - from time to time the protocol stops. When I resubmit it continues > working. > But the question is why does that happen: problem with my dataset and/or > bug? > > > 2.2 optical alignment > > - if you may remember the problem was that it finished because of an error > in 1 file. > > Is there already the solution for skipping the movies that causing the > error? > > Alternatively, I removed that file (it looked fine in terms of frames and > visibility - I can send it for the analysis) and have to rerun the > xmipp3-correlation again. But there is no guarantee that the program will > not stop on some other file. > > > > 3. grigoriefflab - Input - movie stacks > > stops in the beginning with error - > > Input stack filename > 14274: [Runs/022622_ProtUnblur/tmp/movie_000010/FoilHole_ > 26594251_Data_25564934_25564935_20160826_2014-21929.mrc] : 24 > 14275: > 14276: No Such File - please enter a valid filename > > > > > [image: Встроенное изображение 2] > > > > Sincerely, > Dmitry > > > ------------------------------------------------------------ > ------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > |
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From: Dmitry S. <sem...@gm...> - 2017-04-29 09:35:49
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Dear colleagues, The issue is again with movie correction scripts. 1. Motioncorr2 As input, I use the movie stacks (can I use corrected movies as an input to increase the quality - for example after xmipp3-correlation alignment or it will be repetition?) and get the error - ProgrammingError: Incorrect number of bindings supplied. The current statement uses 32, and there are 22 supplied. (the git was updated) [image: Встроенное изображение 1] How can I fix that? 2. xmipp3 - correlation alignment / optical alignment 2.1 correlation alignment - from time to time the protocol stops. When I resubmit it continues working. But the question is why does that happen: problem with my dataset and/or bug? 2.2 optical alignment - if you may remember the problem was that it finished because of an error in 1 file. Is there already the solution for skipping the movies that causing the error? Alternatively, I removed that file (it looked fine in terms of frames and visibility - I can send it for the analysis) and have to rerun the xmipp3-correlation again. But there is no guarantee that the program will not stop on some other file. 3. grigoriefflab - Input - movie stacks stops in the beginning with error - Input stack filename 14274: [Runs/022622_ProtUnblur/tmp/movie_000010/FoilHole_26594251_Data_25564934_25564935_20160826_2014-21929.mrc] : 24 14275: 14276: No Such File - please enter a valid filename [image: Встроенное изображение 2] Sincerely, Dmitry |
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From: Roberto M. <ro...@cn...> - 2017-04-28 16:27:49
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Hi Valérie,
Did you compile the code or install the binary distribution?
best wishes
Roberto
On Fri, Apr 28, 2017 at 11:02 AM, Valérie Biou <val...@ib...> wrote:
> Hello
>
>
> the test for 2D classification using CL2D worked and I tried to run the test for 2D classification using Relion
> which failed with an MPI error (see attached log file).
>
> Do you have any suggestion?
> thanks, best regards
>
>
> Valérie Biou
> Laboratoire de Biologie Physico-Chimique des Protéines Membranaires
> UMR 7099 CNRS/Univ. Paris Diderot P7
> Institut de Biologie Physico-Chimique
> 13 rue Pierre et Marie Curie
> 75005 Paris - France
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
>
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