I'm attempting to build the development branch of the source code. To reduce dependencies, I'm trying to build without any of the GUI support using the flags:
--disable-all-apps --disable-gl-apps
It's complaining about a missing dependency:
configure: error: FATAL: libBLT not found. Check config.log. Set LDFLAGS or -- with-BLT-dir.
but the instructions imply that BLT is only necessary for GUIs.
Are there additional arguments that I need to pass to configure?
Malcolm
the other way to build w/o gui support is to exclude the tcl and vtk paths in configure. in other works, only vtk and mni should be included in your configure line.
On Fri, 2012-01-06 at 11:30 -0600, Malcolm Tobias wrote:
I'm attempting to build the development branch of the source code. To reduce dependencies, I'm trying to build without any of the GUI support using the flags:
--disable-all-apps --disable-gl-apps
It's complaining about a missing dependency:
configure: error: FATAL: libBLT not found. Check config.log. Set LDFLAGS or -- with-BLT-dir.
but the instructions imply that BLT is only necessary for GUIs.
Are there additional arguments that I need to pass to configure?
Malcolm
Nick,
Tcl/Tk is installed on the system under /usr/bin so I can't exclude it from my path without breaking things. VTK isn't in my path.
Should the flags to disable the GUI stuff (--disable-all-apps --disable-gl- apps) be considered broken? Any other suggestions for a work-around? Would a copy of my configure output help?
Malcolm
On Saturday 07 January 2012 14:16:06 Nick Schmansky wrote:
the other way to build w/o gui support is to exclude the tcl and vtk paths in configure. in other works, only vtk and mni should be included in your configure line.
On Fri, 2012-01-06 at 11:30 -0600, Malcolm Tobias wrote:
I'm attempting to build the development branch of the source code. To reduce dependencies, I'm trying to build without any of the GUI support using the flags:
--disable-all-apps --disable-gl-apps
It's complaining about a missing dependency:
configure: error: FATAL: libBLT not found. Check config.log. Set LDFLAGS or -- with-BLT-dir.
but the instructions imply that BLT is only necessary for GUIs.
Are there additional arguments that I need to pass to configure?
Malcolm
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
try addong --disable-tcltk-apps to your configure command line.
--disable-all-apps appears to be broken.
send me your config.log file if it still doesnt work.
n.
On Mon, 2012-01-09 at 09:51 -0600, Malcolm Tobias wrote:
Nick,
Tcl/Tk is installed on the system under /usr/bin so I can't exclude it from my path without breaking things. VTK isn't in my path.
Should the flags to disable the GUI stuff (--disable-all-apps --disable-gl- apps) be considered broken? Any other suggestions for a work-around? Would a copy of my configure output help?
Malcolm
On Saturday 07 January 2012 14:16:06 Nick Schmansky wrote:
the other way to build w/o gui support is to exclude the tcl and vtk paths in configure. in other works, only vtk and mni should be included in your configure line.
On Fri, 2012-01-06 at 11:30 -0600, Malcolm Tobias wrote:
I'm attempting to build the development branch of the source code. To reduce dependencies, I'm trying to build without any of the GUI support using the flags:
--disable-all-apps --disable-gl-apps
It's complaining about a missing dependency:
configure: error: FATAL: libBLT not found. Check config.log. Set LDFLAGS or -- with-BLT-dir.
but the instructions imply that BLT is only necessary for GUIs.
Are there additional arguments that I need to pass to configure?
Malcolm
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Nick,
I'm getting the same error:
[root@login002 freesurfer-dev-20120106]# ./configure --disable-all-apps -- disable-gl-apps --disable-tcltk-apps -with-mni-dir=/export/minc-1.4/ --with- vxl-dir=/export/vxl-1.13.0 ... configure: error: FATAL: libBLT not found. Check config.log. Set LDFLAGS or -- with-BLT-dir.
I've attached the config.log. Let me know if the mail-list software blocks it for any reason.
Cheers, Malcolm
On Monday 09 January 2012 11:09:03 Nick Schmansky wrote:
try addong --disable-tcltk-apps to your configure command line.
--disable-all-apps appears to be broken.
send me your config.log file if it still doesnt work.
n.
On Mon, 2012-01-09 at 09:51 -0600, Malcolm Tobias wrote:
Nick,
Tcl/Tk is installed on the system under /usr/bin so I can't exclude it from my path without breaking things. VTK isn't in my path.
Should the flags to disable the GUI stuff (--disable-all-apps --disable-gl- apps) be considered broken? Any other suggestions for a work-around? Would a copy of my configure output help?
Malcolm
On Saturday 07 January 2012 14:16:06 Nick Schmansky wrote:
the other way to build w/o gui support is to exclude the tcl and vtk paths in configure. in other works, only vtk and mni should be included in your configure line.
On Fri, 2012-01-06 at 11:30 -0600, Malcolm Tobias wrote:
I'm attempting to build the development branch of the source code. To reduce dependencies, I'm trying to build without any of the GUI support using the flags:
--disable-all-apps --disable-gl-apps
It's complaining about a missing dependency:
configure: error: FATAL: libBLT not found. Check config.log. Set LDFLAGS or -- with-BLT-dir.
but the instructions imply that BLT is only necessary for GUIs.
Are there additional arguments that I need to pass to configure?
Malcolm
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
malcolm,
can you try using the attached configure.in? you will need to run ./setup_configure, which will create a new configure script. hopefully --disable-all-apps will then work.
n.
On Mon, 2012-01-09 at 11:51 -0600, Malcolm Tobias wrote:
Nick,
I'm getting the same error:
[root@login002 freesurfer-dev-20120106]# ./configure --disable-all-apps -- disable-gl-apps --disable-tcltk-apps -with-mni-dir=/export/minc-1.4/ --with- vxl-dir=/export/vxl-1.13.0 ... configure: error: FATAL: libBLT not found. Check config.log. Set LDFLAGS or -- with-BLT-dir.
I've attached the config.log. Let me know if the mail-list software blocks it for any reason.
Cheers, Malcolm
On Monday 09 January 2012 11:09:03 Nick Schmansky wrote:
try addong --disable-tcltk-apps to your configure command line.
--disable-all-apps appears to be broken.
send me your config.log file if it still doesnt work.
n.
On Mon, 2012-01-09 at 09:51 -0600, Malcolm Tobias wrote:
Nick,
Tcl/Tk is installed on the system under /usr/bin so I can't exclude it from my path without breaking things. VTK isn't in my path.
Should the flags to disable the GUI stuff (--disable-all-apps --disable-gl- apps) be considered broken? Any other suggestions for a work-around? Would a copy of my configure output help?
Malcolm
On Saturday 07 January 2012 14:16:06 Nick Schmansky wrote:
the other way to build w/o gui support is to exclude the tcl and vtk paths in configure. in other works, only vtk and mni should be included in your configure line.
On Fri, 2012-01-06 at 11:30 -0600, Malcolm Tobias wrote:
I'm attempting to build the development branch of the source code. To reduce dependencies, I'm trying to build without any of the GUI support using the flags:
--disable-all-apps --disable-gl-apps
It's complaining about a missing dependency:
configure: error: FATAL: libBLT not found. Check config.log. Set LDFLAGS or -- with-BLT-dir.
but the instructions imply that BLT is only necessary for GUIs.
Are there additional arguments that I need to pass to configure?
Malcolm
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Nick,
With the new configure.in, --disable-all-apps works as advertised.
Thanks!
Malcolm
On Monday 09 January 2012 13:36:37 Nick Schmansky wrote:
malcolm,
can you try using the attached configure.in? you will need to run ./setup_configure, which will create a new configure script. hopefully --disable-all-apps will then work.
n.
On Mon, 2012-01-09 at 11:51 -0600, Malcolm Tobias wrote:
Nick,
I'm getting the same error:
[root@login002 freesurfer-dev-20120106]# ./configure --disable-all-apps -- disable-gl-apps --disable-tcltk-apps -with-mni-dir=/export/minc-1.4/ --with- vxl-dir=/export/vxl-1.13.0 ... configure: error: FATAL: libBLT not found. Check config.log. Set LDFLAGS or -- with-BLT-dir.
I've attached the config.log. Let me know if the mail-list software blocks it for any reason.
Cheers, Malcolm
On Monday 09 January 2012 11:09:03 Nick Schmansky wrote:
try addong --disable-tcltk-apps to your configure command line.
--disable-all-apps appears to be broken.
send me your config.log file if it still doesnt work.
n.
On Mon, 2012-01-09 at 09:51 -0600, Malcolm Tobias wrote:
Nick,
Tcl/Tk is installed on the system under /usr/bin so I can't exclude it from my path without breaking things. VTK isn't in my path.
Should the flags to disable the GUI stuff (--disable-all-apps --disable-gl- apps) be considered broken? Any other suggestions for a work-around? Would a copy of my configure output help?
Malcolm
On Saturday 07 January 2012 14:16:06 Nick Schmansky wrote:
the other way to build w/o gui support is to exclude the tcl and vtk paths in configure. in other works, only vtk and mni should be included in your configure line.
On Fri, 2012-01-06 at 11:30 -0600, Malcolm Tobias wrote:
I'm attempting to build the development branch of the source code. To reduce dependencies, I'm trying to build without any of the GUI support using the flags:
--disable-all-apps --disable-gl-apps
It's complaining about a missing dependency:
configure: error: FATAL: libBLT not found. Check config.log. Set LDFLAGS or -- with-BLT-dir.
but the instructions imply that BLT is only necessary for GUIs.
Are there additional arguments that I need to pass to configure?
Malcolm
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Nick,
While configure now works, I'm getting a build-time error.
It looks like: histo_register/SimpleBaseLib/include/sbl/image/Image.h
has a dependency on OpenCV. I didn't see OpenCV listed on the Developers Guide:
https://surfer.nmr.mgh.harvard.edu/fswiki/DevelopersGuide
Is this a new dependency?
I tried using "--without-opencv" but that generated an error with freeview:
make[2]: Entering directory `/export/src/freesurfer-dev-20120106/freeview' MainWindow.ui -p -o ui_MainWindow.h make[2]: MainWindow.ui: Command not found
Any suggestions?
Malcolm
On Monday 09 January 2012 13:36:37 Nick Schmansky wrote:
malcolm,
can you try using the attached configure.in? you will need to run ./setup_configure, which will create a new configure script. hopefully --disable-all-apps will then work.
n.
On Mon, 2012-01-09 at 11:51 -0600, Malcolm Tobias wrote:
Nick,
I'm getting the same error:
[root@login002 freesurfer-dev-20120106]# ./configure --disable-all-apps -- disable-gl-apps --disable-tcltk-apps -with-mni-dir=/export/minc-1.4/ --with- vxl-dir=/export/vxl-1.13.0 ... configure: error: FATAL: libBLT not found. Check config.log. Set LDFLAGS or -- with-BLT-dir.
I've attached the config.log. Let me know if the mail-list software blocks it for any reason.
Cheers, Malcolm
On Monday 09 January 2012 11:09:03 Nick Schmansky wrote:
try addong --disable-tcltk-apps to your configure command line.
--disable-all-apps appears to be broken.
send me your config.log file if it still doesnt work.
n.
On Mon, 2012-01-09 at 09:51 -0600, Malcolm Tobias wrote:
Nick,
Tcl/Tk is installed on the system under /usr/bin so I can't exclude it from my path without breaking things. VTK isn't in my path.
Should the flags to disable the GUI stuff (--disable-all-apps --disable-gl- apps) be considered broken? Any other suggestions for a work-around? Would a copy of my configure output help?
Malcolm
On Saturday 07 January 2012 14:16:06 Nick Schmansky wrote:
the other way to build w/o gui support is to exclude the tcl and vtk paths in configure. in other works, only vtk and mni should be included in your configure line.
On Fri, 2012-01-06 at 11:30 -0600, Malcolm Tobias wrote:
I'm attempting to build the development branch of the source code. To reduce dependencies, I'm trying to build without any of the GUI support using the flags:
--disable-all-apps --disable-gl-apps
It's complaining about a missing dependency:
configure: error: FATAL: libBLT not found. Check config.log. Set LDFLAGS or -- with-BLT-dir.
but the instructions imply that BLT is only necessary for GUIs.
Are there additional arguments that I need to pass to configure?
Malcolm
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
malcolm,
configure.in had another bug in it. attached is a fix. run setup_configure again to regenerate configure. its been awhile since someone built a non-gui build offsite, so there could be other problems.
n.
On Mon, 2012-01-09 at 15:07 -0600, Malcolm Tobias wrote:
Nick,
While configure now works, I'm getting a build-time error.
It looks like: histo_register/SimpleBaseLib/include/sbl/image/Image.h
has a dependency on OpenCV. I didn't see OpenCV listed on the Developers Guide:
https://surfer.nmr.mgh.harvard.edu/fswiki/DevelopersGuide
Is this a new dependency?
I tried using "--without-opencv" but that generated an error with freeview:
make[2]: Entering directory `/export/src/freesurfer-dev-20120106/freeview' MainWindow.ui -p -o ui_MainWindow.h make[2]: MainWindow.ui: Command not found
Any suggestions?
Malcolm
On Monday 09 January 2012 13:36:37 Nick Schmansky wrote:
malcolm,
can you try using the attached configure.in? you will need to run ./setup_configure, which will create a new configure script. hopefully --disable-all-apps will then work.
n.
On Mon, 2012-01-09 at 11:51 -0600, Malcolm Tobias wrote:
Nick,
I'm getting the same error:
[root@login002 freesurfer-dev-20120106]# ./configure --disable-all-apps -- disable-gl-apps --disable-tcltk-apps -with-mni-dir=/export/minc-1.4/ --with- vxl-dir=/export/vxl-1.13.0 ... configure: error: FATAL: libBLT not found. Check config.log. Set LDFLAGS or -- with-BLT-dir.
I've attached the config.log. Let me know if the mail-list software blocks it for any reason.
Cheers, Malcolm
On Monday 09 January 2012 11:09:03 Nick Schmansky wrote:
try addong --disable-tcltk-apps to your configure command line.
--disable-all-apps appears to be broken.
send me your config.log file if it still doesnt work.
n.
On Mon, 2012-01-09 at 09:51 -0600, Malcolm Tobias wrote:
Nick,
Tcl/Tk is installed on the system under /usr/bin so I can't exclude it from my path without breaking things. VTK isn't in my path.
Should the flags to disable the GUI stuff (--disable-all-apps --disable-gl- apps) be considered broken? Any other suggestions for a work-around? Would a copy of my configure output help?
Malcolm
On Saturday 07 January 2012 14:16:06 Nick Schmansky wrote:
the other way to build w/o gui support is to exclude the tcl and vtk paths in configure. in other works, only vtk and mni should be included in your configure line.
On Fri, 2012-01-06 at 11:30 -0600, Malcolm Tobias wrote: > I'm attempting to build the development branch of the source > code. To reduce dependencies, I'm trying to build without any of > the GUI support using the flags: > > --disable-all-apps > --disable-gl-apps > > It's complaining about a missing dependency: > > configure: error: FATAL: libBLT not found. Check config.log. Set > LDFLAGS or -- with-BLT-dir. > > but the instructions imply that BLT is only necessary for GUIs. > > Are there additional arguments that I need to pass to configure? > > Malcolm
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Malcolm Tobias 314.362.1594
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Nick,
Everything is now building successfully. Thanks for your help!
What do you normally do to test a build? I tried running 'make check' which seemed pretty extensive. While many tests passed:
[root@login002 freesurfer-dev-20120106]# grep PASS make.check.out | wc -l 407
I did have one fail:
ERROR: gauss_4dfp built against shared libg2c! FAIL: test_libg2c
which seemed to stop the test process. Is this something serious or can it be ignored?
Malcolm
On Monday 09 January 2012 15:43:34 Nick Schmansky wrote:
malcolm,
configure.in had another bug in it. attached is a fix. run setup_configure again to regenerate configure. its been awhile since someone built a non-gui build offsite, so there could be other problems.
n.
On Mon, 2012-01-09 at 15:07 -0600, Malcolm Tobias wrote:
Nick,
While configure now works, I'm getting a build-time error.
It looks like: histo_register/SimpleBaseLib/include/sbl/image/Image.h
has a dependency on OpenCV. I didn't see OpenCV listed on the Developers Guide:
https://surfer.nmr.mgh.harvard.edu/fswiki/DevelopersGuide
Is this a new dependency?
I tried using "--without-opencv" but that generated an error with freeview:
make[2]: Entering directory `/export/src/freesurfer-dev-20120106/freeview' MainWindow.ui -p -o ui_MainWindow.h make[2]: MainWindow.ui: Command not found
Any suggestions?
Malcolm
On Monday 09 January 2012 13:36:37 Nick Schmansky wrote:
malcolm,
can you try using the attached configure.in? you will need to run ./setup_configure, which will create a new configure script. hopefully --disable-all-apps will then work.
n.
On Mon, 2012-01-09 at 11:51 -0600, Malcolm Tobias wrote:
Nick,
I'm getting the same error:
[root@login002 freesurfer-dev-20120106]# ./configure --disable-all-apps -- disable-gl-apps --disable-tcltk-apps -with-mni-dir=/export/minc-1.4/ --with- vxl-dir=/export/vxl-1.13.0 ... configure: error: FATAL: libBLT not found. Check config.log. Set LDFLAGS or -- with-BLT-dir.
I've attached the config.log. Let me know if the mail-list software blocks it for any reason.
Cheers, Malcolm
On Monday 09 January 2012 11:09:03 Nick Schmansky wrote:
try addong --disable-tcltk-apps to your configure command line.
--disable-all-apps appears to be broken.
send me your config.log file if it still doesnt work.
n.
On Mon, 2012-01-09 at 09:51 -0600, Malcolm Tobias wrote:
Nick,
Tcl/Tk is installed on the system under /usr/bin so I can't exclude it from my path without breaking things. VTK isn't in my path.
Should the flags to disable the GUI stuff (--disable-all-apps --disable-gl- apps) be considered broken? Any other suggestions for a work-around? Would a copy of my configure output help?
Malcolm
On Saturday 07 January 2012 14:16:06 Nick Schmansky wrote: > the other way to build w/o gui support is to exclude the tcl > and vtk paths in configure. in other works, only vtk and mni > should be included in your configure line. > > On Fri, 2012-01-06 at 11:30 -0600, Malcolm Tobias wrote: > > I'm attempting to build the development branch of the source > > code. To reduce dependencies, I'm trying to build without any > > of the GUI support using the flags: > > > > --disable-all-apps > > --disable-gl-apps > > > > It's complaining about a missing dependency: > > > > configure: error: FATAL: libBLT not found. Check config.log. > > Set LDFLAGS or -- with-BLT-dir. > > > > but the instructions imply that BLT is only necessary for > > GUIs. > > > > Are there additional arguments that I need to pass to > > configure? > > > > Malcolm > > The information in this e-mail is intended only for the person > to whom it is addressed. If you believe this e-mail was sent > to you in error and the e-mail contains patient information, > please contact the Partners Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent > to you in error but does not contain patient information, > please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
malcolm,
running 'make check' is one way to check the build. we run that nightly on our three build platforms (linux 32b, 64b and mac leopard). a goal of our linux centos build is to have it run on as many linux variants as possible without people having to modify their local install, and to that end, we've found that some linux systems dont have libg2c installed, so what we do on our build platforms is to remove the libg2c.so (shared lib) file, leaving the .a (static lib), so that the shared lib dependency is removed. you can either do the same (so far doing so hasnt broken other non-freesurfer apps), or you can skip it.
you should run recon-all -all on 'bert', or any other data you have handy. make sure it runs to completion without error. checking the accuracy of the results against known prior runs is possible (we do this locally) but probably not necessary in your case, as your results might be different (due to platform differences) but not 'wrong'. mainly you want to make sure recon-all doesnt hit some strange runtime problem (missing lib or whatnot). remember you shouldn't mix results from your new platform with results from other platforms when conducting a group study (ie always do groups studies using results from the same platform and version).
n
On Tue, 2012-01-10 at 07:47 -0600, Malcolm Tobias wrote:
Nick,
Everything is now building successfully. Thanks for your help!
What do you normally do to test a build? I tried running 'make check' which seemed pretty extensive. While many tests passed:
[root@login002 freesurfer-dev-20120106]# grep PASS make.check.out | wc -l 407
I did have one fail:
ERROR: gauss_4dfp built against shared libg2c! FAIL: test_libg2c
which seemed to stop the test process. Is this something serious or can it be ignored?
Malcolm
On Monday 09 January 2012 15:43:34 Nick Schmansky wrote:
malcolm,
configure.in had another bug in it. attached is a fix. run setup_configure again to regenerate configure. its been awhile since someone built a non-gui build offsite, so there could be other problems.
n.
On Mon, 2012-01-09 at 15:07 -0600, Malcolm Tobias wrote:
Nick,
While configure now works, I'm getting a build-time error.
It looks like: histo_register/SimpleBaseLib/include/sbl/image/Image.h
has a dependency on OpenCV. I didn't see OpenCV listed on the Developers Guide:
https://surfer.nmr.mgh.harvard.edu/fswiki/DevelopersGuide
Is this a new dependency?
I tried using "--without-opencv" but that generated an error with freeview:
make[2]: Entering directory `/export/src/freesurfer-dev-20120106/freeview' MainWindow.ui -p -o ui_MainWindow.h make[2]: MainWindow.ui: Command not found
Any suggestions?
Malcolm
On Monday 09 January 2012 13:36:37 Nick Schmansky wrote:
malcolm,
can you try using the attached configure.in? you will need to run ./setup_configure, which will create a new configure script. hopefully --disable-all-apps will then work.
n.
On Mon, 2012-01-09 at 11:51 -0600, Malcolm Tobias wrote:
Nick,
I'm getting the same error:
[root@login002 freesurfer-dev-20120106]# ./configure --disable-all-apps -- disable-gl-apps --disable-tcltk-apps -with-mni-dir=/export/minc-1.4/ --with- vxl-dir=/export/vxl-1.13.0 ... configure: error: FATAL: libBLT not found. Check config.log. Set LDFLAGS or -- with-BLT-dir.
I've attached the config.log. Let me know if the mail-list software blocks it for any reason.
Cheers, Malcolm
On Monday 09 January 2012 11:09:03 Nick Schmansky wrote:
try addong --disable-tcltk-apps to your configure command line.
--disable-all-apps appears to be broken.
send me your config.log file if it still doesnt work.
n.
On Mon, 2012-01-09 at 09:51 -0600, Malcolm Tobias wrote: > Nick, > > Tcl/Tk is installed on the system under /usr/bin so I can't > exclude it from my path without breaking things. VTK isn't in > my path. > > Should the flags to disable the GUI stuff (--disable-all-apps > --disable-gl- apps) be considered broken? Any other suggestions > for a work-around? Would a copy of my configure output help? > > Malcolm > > On Saturday 07 January 2012 14:16:06 Nick Schmansky wrote: > > the other way to build w/o gui support is to exclude the tcl > > and vtk paths in configure. in other works, only vtk and mni > > should be included in your configure line. > > > > On Fri, 2012-01-06 at 11:30 -0600, Malcolm Tobias wrote: > > > I'm attempting to build the development branch of the source > > > code. To reduce dependencies, I'm trying to build without any > > > of the GUI support using the flags: > > > > > > --disable-all-apps > > > --disable-gl-apps > > > > > > It's complaining about a missing dependency: > > > > > > configure: error: FATAL: libBLT not found. Check config.log. > > > Set LDFLAGS or -- with-BLT-dir. > > > > > > but the instructions imply that BLT is only necessary for > > > GUIs. > > > > > > Are there additional arguments that I need to pass to > > > configure? > > > > > > Malcolm > > > > The information in this e-mail is intended only for the person > > to whom it is addressed. If you believe this e-mail was sent > > to you in error and the e-mail contains patient information, > > please contact the Partners Compliance HelpLine at > > http://www.partners.org/complianceline . If the e-mail was sent > > to you in error but does not contain patient information, > > please contact the sender and properly dispose of the e-mail.
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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Nick,
I ran recon-all on bert and it did produce an error:
recon-all -s ernie exited with ERRORS at Tue Jan 10 18:47:07 CST 2012
A cursory glance at the recon-all.log showed:
********************************************************** * * WARNING: Registration did not converge in 5 steps! * Problem might be ill posed. * Please inspect output manually! * **********************************************************
I'm not sure if that's the real problem or whether it occurs further down in the logs. I've attached the entire log.
Malcolm
On Tuesday 10 January 2012 10:58:21 Nick Schmansky wrote:
malcolm,
running 'make check' is one way to check the build. we run that nightly on our three build platforms (linux 32b, 64b and mac leopard). a goal of our linux centos build is to have it run on as many linux variants as possible without people having to modify their local install, and to that end, we've found that some linux systems dont have libg2c installed, so what we do on our build platforms is to remove the libg2c.so (shared lib) file, leaving the .a (static lib), so that the shared lib dependency is removed. you can either do the same (so far doing so hasnt broken other non-freesurfer apps), or you can skip it.
you should run recon-all -all on 'bert', or any other data you have handy. make sure it runs to completion without error. checking the accuracy of the results against known prior runs is possible (we do this locally) but probably not necessary in your case, as your results might be different (due to platform differences) but not 'wrong'. mainly you want to make sure recon-all doesnt hit some strange runtime problem (missing lib or whatnot). remember you shouldn't mix results from your new platform with results from other platforms when conducting a group study (ie always do groups studies using results from the same platform and version).
n
On Tue, 2012-01-10 at 07:47 -0600, Malcolm Tobias wrote:
Nick,
Everything is now building successfully. Thanks for your help!
What do you normally do to test a build? I tried running 'make check' which seemed pretty extensive. While many tests passed:
[root@login002 freesurfer-dev-20120106]# grep PASS make.check.out | wc -l 407
I did have one fail:
ERROR: gauss_4dfp built against shared libg2c! FAIL: test_libg2c
which seemed to stop the test process. Is this something serious or can it be ignored?
Malcolm
On Monday 09 January 2012 15:43:34 Nick Schmansky wrote:
malcolm,
configure.in had another bug in it. attached is a fix. run setup_configure again to regenerate configure. its been awhile since someone built a non-gui build offsite, so there could be other problems.
n.
On Mon, 2012-01-09 at 15:07 -0600, Malcolm Tobias wrote:
Nick,
While configure now works, I'm getting a build-time error.
It looks like: histo_register/SimpleBaseLib/include/sbl/image/Image.h
has a dependency on OpenCV. I didn't see OpenCV listed on the Developers Guide:
https://surfer.nmr.mgh.harvard.edu/fswiki/DevelopersGuide
Is this a new dependency?
I tried using "--without-opencv" but that generated an error with freeview:
make[2]: Entering directory `/export/src/freesurfer-dev-20120106/freeview' MainWindow.ui -p -o ui_MainWindow.h make[2]: MainWindow.ui: Command not found
Any suggestions?
Malcolm
On Monday 09 January 2012 13:36:37 Nick Schmansky wrote:
malcolm,
can you try using the attached configure.in? you will need to run ./setup_configure, which will create a new configure script. hopefully --disable-all-apps will then work.
n.
On Mon, 2012-01-09 at 11:51 -0600, Malcolm Tobias wrote:
Nick,
I'm getting the same error:
[root@login002 freesurfer-dev-20120106]# ./configure --disable-all-apps -- disable-gl-apps --disable-tcltk-apps -with-mni-dir=/export/minc-1.4/ --with- vxl-dir=/export/vxl-1.13.0 ... configure: error: FATAL: libBLT not found. Check config.log. Set LDFLAGS or -- with-BLT-dir.
I've attached the config.log. Let me know if the mail-list software blocks it for any reason.
Cheers, Malcolm
On Monday 09 January 2012 11:09:03 Nick Schmansky wrote: > try addong --disable-tcltk-apps to your configure command > line. > > --disable-all-apps appears to be broken. > > send me your config.log file if it still doesnt work. > > n. > > On Mon, 2012-01-09 at 09:51 -0600, Malcolm Tobias wrote: > > Nick, > > > > Tcl/Tk is installed on the system under /usr/bin so I can't > > exclude it from my path without breaking things. VTK isn't > > in my path. > > > > Should the flags to disable the GUI stuff (--disable-all-apps > > --disable-gl- apps) be considered broken? Any other > > suggestions for a work-around? Would a copy of my configure > > output help? > > > > Malcolm > > > > On Saturday 07 January 2012 14:16:06 Nick Schmansky wrote: > > > the other way to build w/o gui support is to exclude the > > > tcl and vtk paths in configure. in other works, only vtk > > > and mni should be included in your configure line. > > > > > > On Fri, 2012-01-06 at 11:30 -0600, Malcolm Tobias wrote: > > > > I'm attempting to build the development branch of the > > > > source code. To reduce dependencies, I'm trying to build > > > > without any of the GUI support using the flags: > > > > > > > > --disable-all-apps > > > > --disable-gl-apps > > > > > > > > It's complaining about a missing dependency: > > > > > > > > configure: error: FATAL: libBLT not found. Check > > > > config.log. Set LDFLAGS or -- with-BLT-dir. > > > > > > > > but the instructions imply that BLT is only necessary for > > > > GUIs. > > > > > > > > Are there additional arguments that I need to pass to > > > > configure? > > > > > > > > Malcolm > > > > > > The information in this e-mail is intended only for the > > > person to whom it is addressed. If you believe this e-mail > > > was sent to you in error and the e-mail contains patient > > > information, please contact the Partners Compliance > > > HelpLine at http://www.partners.org/complianceline . If > > > the e-mail was sent to you in error but does not contain > > > patient information, please contact the sender and > > > properly dispose of the e-mail. > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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malcolm,
hi, i'm able to replicate that warning on that data, and i'm investigating. i would say its a false alarm, as that input data is considered 'optimal' (mprage from our own scanners).
it appears the recon-all proceeded successfully all the way to nearly the end. it failed in some new code (you are working with our 'development' checkout, so new stuff often breaks the stream), so i'll have to pass that failure along to that developer (thanks for catching that!).
so i think your build seems fine. i notice you are running on a somewhat standard linux platform. does the centos binary build that we distribute not suit your needs? just wanted to make sure you werent under the impression that you have to build from scratch if you arent running centos (people have made assumption in the past). the centos build seems to run fine on nearly all x86 linux variants, sometimes with some library tweeking. its a help though to have developers such as yourself build the source.
n.
On Wed, 2012-01-11 at 07:53 -0600, Malcolm Tobias wrote:
Nick,
I ran recon-all on bert and it did produce an error:
recon-all -s ernie exited with ERRORS at Tue Jan 10 18:47:07 CST 2012
A cursory glance at the recon-all.log showed:
- WARNING: Registration did not converge in 5 steps!
Problem might be ill posed.Please inspect output manually!
I'm not sure if that's the real problem or whether it occurs further down in the logs. I've attached the entire log.
Malcolm
On Tuesday 10 January 2012 10:58:21 Nick Schmansky wrote:
malcolm,
running 'make check' is one way to check the build. we run that nightly on our three build platforms (linux 32b, 64b and mac leopard). a goal of our linux centos build is to have it run on as many linux variants as possible without people having to modify their local install, and to that end, we've found that some linux systems dont have libg2c installed, so what we do on our build platforms is to remove the libg2c.so (shared lib) file, leaving the .a (static lib), so that the shared lib dependency is removed. you can either do the same (so far doing so hasnt broken other non-freesurfer apps), or you can skip it.
you should run recon-all -all on 'bert', or any other data you have handy. make sure it runs to completion without error. checking the accuracy of the results against known prior runs is possible (we do this locally) but probably not necessary in your case, as your results might be different (due to platform differences) but not 'wrong'. mainly you want to make sure recon-all doesnt hit some strange runtime problem (missing lib or whatnot). remember you shouldn't mix results from your new platform with results from other platforms when conducting a group study (ie always do groups studies using results from the same platform and version).
n
On Tue, 2012-01-10 at 07:47 -0600, Malcolm Tobias wrote:
Nick,
Everything is now building successfully. Thanks for your help!
What do you normally do to test a build? I tried running 'make check' which seemed pretty extensive. While many tests passed:
[root@login002 freesurfer-dev-20120106]# grep PASS make.check.out | wc -l 407
I did have one fail:
ERROR: gauss_4dfp built against shared libg2c! FAIL: test_libg2c
which seemed to stop the test process. Is this something serious or can it be ignored?
Malcolm
On Monday 09 January 2012 15:43:34 Nick Schmansky wrote:
malcolm,
configure.in had another bug in it. attached is a fix. run setup_configure again to regenerate configure. its been awhile since someone built a non-gui build offsite, so there could be other problems.
n.
On Mon, 2012-01-09 at 15:07 -0600, Malcolm Tobias wrote:
Nick,
While configure now works, I'm getting a build-time error.
It looks like: histo_register/SimpleBaseLib/include/sbl/image/Image.h
has a dependency on OpenCV. I didn't see OpenCV listed on the Developers Guide:
https://surfer.nmr.mgh.harvard.edu/fswiki/DevelopersGuide
Is this a new dependency?
I tried using "--without-opencv" but that generated an error with freeview:
make[2]: Entering directory `/export/src/freesurfer-dev-20120106/freeview' MainWindow.ui -p -o ui_MainWindow.h make[2]: MainWindow.ui: Command not found
Any suggestions?
Malcolm
On Monday 09 January 2012 13:36:37 Nick Schmansky wrote:
malcolm,
can you try using the attached configure.in? you will need to run ./setup_configure, which will create a new configure script. hopefully --disable-all-apps will then work.
n.
On Mon, 2012-01-09 at 11:51 -0600, Malcolm Tobias wrote: > Nick, > > I'm getting the same error: > > [root@login002 freesurfer-dev-20120106]# ./configure > --disable-all-apps -- disable-gl-apps --disable-tcltk-apps > -with-mni-dir=/export/minc-1.4/ --with- > vxl-dir=/export/vxl-1.13.0 ... > configure: error: FATAL: libBLT not found. Check config.log. Set > LDFLAGS or -- with-BLT-dir. > > I've attached the config.log. Let me know if the mail-list > software blocks it for any reason. > > Cheers, > Malcolm > > On Monday 09 January 2012 11:09:03 Nick Schmansky wrote: > > try addong --disable-tcltk-apps to your configure command > > line. > > > > --disable-all-apps appears to be broken. > > > > send me your config.log file if it still doesnt work. > > > > n. > > > > On Mon, 2012-01-09 at 09:51 -0600, Malcolm Tobias wrote: > > > Nick, > > > > > > Tcl/Tk is installed on the system under /usr/bin so I can't > > > exclude it from my path without breaking things. VTK isn't > > > in my path. > > > > > > Should the flags to disable the GUI stuff (--disable-all-apps > > > --disable-gl- apps) be considered broken? Any other > > > suggestions for a work-around? Would a copy of my configure > > > output help? > > > > > > Malcolm > > > > > > On Saturday 07 January 2012 14:16:06 Nick Schmansky wrote: > > > > the other way to build w/o gui support is to exclude the > > > > tcl and vtk paths in configure. in other works, only vtk > > > > and mni should be included in your configure line. > > > > > > > > On Fri, 2012-01-06 at 11:30 -0600, Malcolm Tobias wrote: > > > > > I'm attempting to build the development branch of the > > > > > source code. To reduce dependencies, I'm trying to build > > > > > without any of the GUI support using the flags: > > > > > > > > > > --disable-all-apps > > > > > --disable-gl-apps > > > > > > > > > > It's complaining about a missing dependency: > > > > > > > > > > configure: error: FATAL: libBLT not found. Check > > > > > config.log. Set LDFLAGS or -- with-BLT-dir. > > > > > > > > > > but the instructions imply that BLT is only necessary for > > > > > GUIs. > > > > > > > > > > Are there additional arguments that I need to pass to > > > > > configure? > > > > > > > > > > Malcolm > > > > > > > > The information in this e-mail is intended only for the > > > > person to whom it is addressed. If you believe this e-mail > > > > was sent to you in error and the e-mail contains patient > > > > information, please contact the Partners Compliance > > > > HelpLine at http://www.partners.org/complianceline . If > > > > the e-mail was sent to you in error but does not contain > > > > patient information, please contact the sender and > > > > properly dispose of the e-mail. > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Nick,
On Wednesday 11 January 2012 11:52:19 Nick Schmansky wrote:
it appears the recon-all proceeded successfully all the way to nearly the end. it failed in some new code (you are working with our 'development' checkout, so new stuff often breaks the stream), so i'll have to pass that failure along to that developer (thanks for catching that!).
Thanks for checking on this. I have to rely on you guys for verification that the code is producing the correct results as I'm clueless about the science behind FreeSurfer. I was pleasantly surprised at the extensive level of tests during "make check". More scientific applications should strive for this level of testing.
so i think your build seems fine. i notice you are running on a somewhat standard linux platform. does the centos binary build that we distribute not suit your needs?
The distributed binary works fine, but, we've got dozens of FreeSurfer users who sometimes submit hundreds of runs, so I'm hoping that any performance benefits we could squeeze out would have a big impact on our community. On top of that, we have members of the Human Connectome Project using our cluster so it's possible that they'll need bleeding-edge versions of FreeSurfer in the future.
As an aside, the distributed binary ran for me in 11:41, where the custom built version ran in 10:44. It's impossible to say whether this was due to building from scratch or a result of using the development branch.
My real goal is to revisit building with the Intel compilers (which I bugged you about 1 year ago). I'm close, but that should be a topic for a different thread ;-)
Cheers, Malcolm
freesurfer@nmr.mgh.harvard.edu
-
Malcolm Tobias -
Nick Schmansky