Build Error: make: *** [all] Error 2

[dougbevan]

Attempting to build on new cluster, can't build with FFTW/FLTK enabled.

Please write a clear description of what the problem is.

Environment:

• OS: CentOS 7.7
• MPI runtime: Have tried 4.0.3, 3.1.3, 1.10.7
• Cmake: 3.17.0
• gcc: 4.8.5
• cuda: 10.1.243
• RELION version Relion 3.1-beta-commit-6d9a0d
• Memory: 512GB headnode / 512GB worker nodes
• GPU: 2080 Ti

Error message:

......
Making install in tools
/usr/bin/mkdir -p '/opt/cryoem/relion/external/fftw/bin'
/usr/bin/mkdir -p '/opt/cryoem/relion/external/fftw/bin'
/usr/bin/mkdir -p '/opt/cryoem/relion/external/fftw/share/man/man1'
/usr/bin/install -c fftw-wisdom-to-conf '/opt/cryoem/relion/external/fftw/bin'
/bin/sh ../libtool --mode=install /usr/bin/install -c fftw-wisdom '/opt/cryoem/relion/external/fftw/bin'
/usr/bin/install -c -m 644 fftw-wisdom-to-conf.1 fftw-wisdom.1 '/opt/cryoem/relion/external/fftw/share/man/man1'
libtool: install: /usr/bin/install -c .libs/fftw-wisdom /opt/cryoem/relion/external/fftw/bin/fftw-wisdom
Making install in m4
[ 5%] Completed 'own_fftw_lib'
[ 5%] Built target own_fftw_lib
make: *** [all] Error 2
........

Thanks for any advice that helps!

[biochem-fan]

Please try again with make -j1. Otherwise, the order of messages is messed up.

[dougbevan]

Thanks -- that makes sense of course.

Also here, I'm switching to a newer gcc (8.2.0). Can switch back if needed, but the error seems the same...

Compiling forms_compatability.cxx...
Compiling forms_bitmap.cxx...
Compiling forms_free.cxx...
Compiling forms_fselect.cxx...
Compiling forms_pixmap.cxx...
Compiling forms_timer.cxx...
/cm/shared/apps/gcc8/8.2.0/bin/gcc-ar cr ../lib/libfltk_forms.a ...
/cm/shared/apps/gcc8/8.2.0/bin/g++ -L. -Wl,-no-undefined -Wl,-Bsymbolic-functions -Wl,-gc-sections -Wl,-soname,libfltk_forms.so.1.3 -lXrender -lXfixes -lXext -lXft -lfontconfig -lpthread -ldl -lm -lX11 -shared -fPIC -o libfltk_forms.so.1.3 ...
Compiling Fl_Gl_Choice.cxx...
Fl_Gl_Choice.cxx: In function ‘__GLXcontextRec* fl_create_gl_context(Fl_Window*, const Fl_Gl_Choice*)’:
Fl_Gl_Choice.cxx:335:7: error: ‘GLX_CONTEXT_MAJOR_VERSION_ARB’ was not declared in this scope
GLX_CONTEXT_MAJOR_VERSION_ARB, 3,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Fl_Gl_Choice.cxx:335:7: note: suggested alternative: ‘FL_MAJOR_VERSION’
GLX_CONTEXT_MAJOR_VERSION_ARB, 3,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
FL_MAJOR_VERSION
Fl_Gl_Choice.cxx:336:7: error: ‘GLX_CONTEXT_MINOR_VERSION_ARB’ was not declared in this scope
GLX_CONTEXT_MINOR_VERSION_ARB, 2,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Fl_Gl_Choice.cxx:336:7: note: suggested alternative: ‘GLX_GLXEXT_VERSION’
GLX_CONTEXT_MINOR_VERSION_ARB, 2,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
GLX_GLXEXT_VERSION
make[4]: *** [Fl_Gl_Choice.o] Error 1
make[3]: *** [all] Error 1
make[2]: *** [OWN_FLTK-prefix/src/OWN_FLTK-stamp/OWN_FLTK-build] Error 2
make[1]: *** [CMakeFiles/OWN_FLTK.dir/all] Error 2
make: *** [all] Error 2

[biochem-fan]

Probably you need OpenGL related header files. Although RELION does not use OpenGL, FLTK apparently needs it for compilation. I cannot tell which file is missing. You (or IT admin) have to compare the libraries installed in your old cluster and the new cluster.

[dougbevan]

I'm the IT admin, so I can install whatever is needed. The clusters are different OS versions, so the comparisons aren't exact.

You mean OpenGL as in freeglut? Both freeglut and freeglut-devel are installed, which matches what we have on our older (working) system...

freeglut.x86_64 3.0.0-8.el7 @base
freeglut-devel.x86_64 3.0.0-8.el7 @base

[biochem-fan]

‘GLX_CONTEXT_MAJOR_VERSION_ARB is defined in /usr/include/GL/gl.h (or something included therein), which comes with libgl-dev. Can you make sure you have this? Also make sure the compiler is not finding the same file provided from other sources (e.g. conda).

Some computing cluster do not have libraries for X Window and that causes a problem. If your log-in node (or an interactive node) have X, try compiling there.

[dougbevan]

Thanks for clarifying.

• x window libs are installed (compiling on the head node, can verify with xeyes, other gui's)

• I do have gl.h under /usr/include/GL/

[root@vision GL]# ls -lah
total 1.7M
drwxr-xr-x 3 root root 4.0K Feb 11 12:12 .
drwxr-xr-x 87 root root 8.0K Feb 17 12:49 ..
-rw-r--r-- 1 root root 11K Oct 17 2014 freeglut_ext.h
-rw-r--r-- 1 root root 681 Oct 21 2003 freeglut.h
-rw-r--r-- 1 root root 27K Oct 17 2014 freeglut_std.h
-rw-r--r-- 1 root root 401K Feb 4 17:59 glcorearb.h
-rw-r--r-- 1 root root 813K Feb 4 17:59 glext.h
-rw-r--r-- 1 root root 79K Feb 4 17:59 gl.h
-rw-r--r-- 1 root root 156K Feb 4 17:59 gl_mangle.h
-rw-r--r-- 1 root root 17K Jun 10 2014 glu.h
-rw-r--r-- 1 root root 3.3K Jun 10 2014 glu_mangle.h
-rw-r--r-- 1 root root 639 Oct 21 2003 glut.h
-rw-r--r-- 1 root root 47K Feb 4 17:59 glxext.h
-rw-r--r-- 1 root root 15K Feb 4 17:59 glx.h
-rw-r--r-- 1 root root 4.6K Oct 30 2018 glxint.h
-rw-r--r-- 1 root root 3.4K Feb 4 17:59 glx_mangle.h
-rw-r--r-- 1 root root 2.1K Oct 30 2018 glxmd.h
-rw-r--r-- 1 root root 80K Oct 30 2018 glxproto.h
-rw-r--r-- 1 root root 12K Oct 30 2018 glxtokens.h
drwxr-xr-x 2 root root 43 Feb 11 12:12 internal

• I don't see any other gl.h et all in the path that would interfere here

Thanks for the help!

[biochem-fan]

Hmm, this is difficult. Our cluster uses Scientific Linux 7.7, which should be similar to Cent OS 7.7.

[dougbevan]

Yes, that should be extremely similar.

I installed the system FLTK from yum on the head node, and was able to build --with FFTW using the system FLTK. I suppose that is ok, I'm still curious as to whey this didn't work. Any thoughts appreciated.