Hi,
I am trying to compile cisTEM to run on a campus cluster. I have been able to run configure without problems. However, when I try the make command, I get:
cd . && /bin/sh /N/soft/rhel6/cryoem/Grigorieff/cisTEM/cistem-1.0.0-beta/missing automake-1.13 --gnu
/N/soft/rhel6/cryoem/Grigorieff/cisTEM/cistem-1.0.0-beta/missing: line 81: automake-1.13: command not found
WARNING: 'automake-1.13' is missing on your system.
You should only need it if you modified 'Makefile.am' or
'configure.ac' or m4 files included by 'configure.ac'.
The 'automake' program is part of the GNU Automake package:
<http://www.gnu.org/software/automake>
It also requires GNU Autoconf, GNU m4 and Perl in order to run:
<http://www.gnu.org/software/autoconf>
<http://www.gnu.org/software/m4/>
<http://www.perl.org/>
make: *** [Makefile.in] Error 1
We have automake-1.14 on this system, but it would be really difficult for me to add version 1.13. Is there a way around this?
Any help would be appreciated.
Hi David,
Firstly - Is there a reason that you cannot use the precompiled binaries? These will probably be a lot faster than a version you compile yourself (perhaps up to 5 times faster).
Secondly - That error is strange as you shouldn't need those programs unless you changed the configure.ac or Makefile.am. You may be able to recover by typing :-
in the directory.
Tim
Tim,
I usually find that compiling on the cluster platform I intend to use solves a host of unexpected run-time problems. I will try the precompiled binaries and see what happens.
Why are your precompiled binaries that much faster than what I can compile locally?
All I did was run configure and then make, so I was complely puzzled by the error also. I will try autoreconf and let you know what happens.
Hi David,
Basically, if you use the intel compiler and link against the MKL you should get equal speed, but most people don't have them.
Tim
Tim,
I do have those (one of the advantages of running on a cluster), so maybe I will try that. If I can get the issues with compiling solved...
I did try autoreconf:
$ autoreconf
aclocal: warning: couldn't open directory 'm4': No such file or directory
configure.ac:2: error: Autoconf version 2.65 or higher is required
/N/soft/rhel6/automake/1.14.1/share/aclocal-1.14/init.m4:29: AM_INIT_AUTOMAKE is expanded from...
configure.ac:2: the top level
autom4te: /usr/bin/m4 failed with exit status: 63
aclocal: error: echo failed with exit status: 63
autoreconf: aclocal failed with exit status: 63
I was able to find and use autoconf 2.69, but got a different error:
$ autoreconf
aclocal: warning: couldn't open directory 'm4': No such file or directory
configure.ac:14: error: possibly undefined macro: AC_LIBTOOL_DLOPEN
If this token and others are legitimate, please use m4_pattern_allow.
See the Autoconf documentation.
configure.ac:15: error: possibly undefined macro: AC_PROG_LIBTOOL
autoreconf: /N/soft/rhel6/autoconf/2.6.9/bin/autoconf failed with exit status: 1
Hi David,
Those errors should be fixed by running :-
Tim
Tim,
That seems to have gotten me someplace useful, but I have to run to a meeting and won't get back to this until later today. Thanks.
Tim,
I ran into one final issue, but I fixed it and as far as I can tell, things have finally compiled. The issue is that my system libtool is version 2.2.6b but teh configure command creates a libtool binary that is version 2.4.2. Near the end of the make command, I ran into a libtool version error where the make command inside the src directory was deliberately looking for ../libtool.
Once I realized that was the issue, I simply copied the system libtool to that location (the main source directory). It now all seems to have run smoothly. I will run through the tutorial later in the week and let you know whether it actually works.
Thanks for all the help.