Comments (23)
The exact commands for the build were:
git clone [email protected]:omnia-md/virtual-machines.git
cd virtual-machines/linux/
vagrant up
vagrant ssh
export PATH=$HOME/miniconda/bin:$PATH
sudo yum install gcc-gfortran
git clone https://github.com/omnia-md/conda-recipes.git
cd conda-recipes
conda build ambermini
from ambermini.
What version of gcc-gfortran did you install? On the VM, after building ambermini
, try installing it and then running ldd
on one of the shared object files. One of the lines listed should be libc.so.6
, and then you can run readelf
on that to see what version the symbols are:
e.g.
readelf -Ws /lib/x86_64-linux-gnu/libc.so.6 | grep GLIBC
from ambermini.
Upgrading your compiler toolchain is going to upgrade your libc/libstdc++, which is probably not what you want, given that the point of these VMs is to link against older versions of the symbols.
from ambermini.
The Version history table here http://en.wikipedia.org/wiki/GNU_C_Library is particularly useful, since it gives you the canonical glibc version for each rhel/debian release.
from ambermini.
Yeah, I somehow thought I had already this VM set up to work properly...
[vagrant@localhost ~]$ gfortran -v
Using built-in specs.
Target: x86_64-redhat-linux
Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-languages=c,c++,objc,obj-c++,java,fortran,ada --enable-java-awt=gtk --disable-dssi --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-1.5.0.0/jre --enable-libgcj-multifile --enable-java-maintainer-mode --with-ecj-jar=/usr/share/java/eclipse-ecj.jar --disable-libjava-multilib --with-ppl --with-cloog --with-tune=generic --with-arch_32=i686 --build=x86_64-redhat-linux
Thread model: posix
gcc version 4.4.7 20120313 (Red Hat 4.4.7-11) (GCC)
from ambermini.
OK, I think the issue is that my VM is now 6.6:
[vagrant@localhost ~]$ cat /etc/centos-release
CentOS release 6.6 (Final)
from ambermini.
Can you post the output of readelf
on the libc.so
?
from ambermini.
https://gist.github.com/kyleabeauchamp/dcd6c82b8ab2b006dc3b
from ambermini.
Can you also post ldd --version
?
from ambermini.
[vagrant@localhost ~]$ ldd --version
ldd (GNU libc) 2.12
Copyright (C) 2010 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
Written by Roland McGrath and Ulrich Drepper.
from ambermini.
And yet the binaries you made on this machine were actually crapping out, saying 'GLIBC_2.14' not found
? That doesn't seem right.
from ambermini.
My bad
from ambermini.
I think it may have been due to binstar's refusal to overwrite packages during upload. Not sure. Regardless, fixed.
from ambermini.
No, there actually is something messed up in the current conda package for omnia/ambermini:
cd omniaambermini
# https://binstar.org/omnia/ambermini/14.0.1/download/linux-64/ambermini-14.0.1-0.tar.bz2
tar -jxvf linux-64_ambermini-14.0.1-0.tar.bz2
readelf -Ws ./bin/parmchk2_pvt |grep GLIBC|grep 14
cd ../kyleambermini
# https://binstar.org/kyleabeauchamp/ambermini/14.0.1/download/linux-64/ambermini-14.0.1-0.tar.bz2
tar -jxvf linux-64_ambermini-14.0.1-0.tar.bz2
readelf -Ws ./bin/parmchk2_pvt |grep GLIBC|grep 14
kyleb@kyleb-DX4870:~/src/Software/omniambermini$ readelf -Ws ./bin/parmchk2_pvt |grep GLIBC|grep 14
14: 0000000000000000 0 FUNC GLOBAL DEFAULT UND modf@GLIBC_2.2.5 (3)
29: 0000000000000000 0 FUNC GLOBAL DEFAULT UND memcpy@GLIBC_2.14 (5)
140: 0000000000000000 0 FUNC GLOBAL DEFAULT UND fopen64@@GLIBC_2.2.5
142: 0000000000000000 0 FUNC GLOBAL DEFAULT UND memcpy@@GLIBC_2.14
214: 0000000000000000 0 FUNC GLOBAL DEFAULT UND fwrite@@GLIBC_2.2.5
kyleb@kyleb-DX4870:~/src/Software/kyleambermini$ readelf -Ws ./bin/parmchk2_pvt |grep GLIBC|grep 14
14: 0000000000000000 0 FUNC GLOBAL DEFAULT UND system@GLIBC_2.2.5 (3)
141: 0000000000000000 0 FUNC GLOBAL DEFAULT UND fputs@@GLIBC_2.2.5
147: 0000000000000000 0 FUNC GLOBAL DEFAULT UND atoi@@GLIBC_2.2.5
from ambermini.
If someone else can verify that my new conda package works, I can upload it to the omnia conda repo.
from ambermini.
Here are some more command lines if people want to do tests on a fresh miniconda:
MINICONDA=Miniconda-latest-Linux-x86_64.sh
wget http://repo.continuum.io/miniconda/$MINICONDA
bash Miniconda-latest-Linux-x86_64.sh
./miniconda/bin/conda install -c https://conda.binstar.org/omnia ambermini
MINICONDA=Miniconda-latest-Linux-x86_64.sh
wget http://repo.continuum.io/miniconda/$MINICONDA
bash Miniconda-latest-Linux-x86_64.sh
./miniconda/bin/conda install -c https://conda.binstar.org/kyleabeauchamp ambermini
from ambermini.
Tried it.
The Omnia one is broken when I try it on a fresh miniconda install. Kyle's one does work. (Centos 6.4, hal.cbio.mskcc.org)
from ambermini.
Is this something I can try to automate the building of now?
from ambermini.
Sure, I have my exact command lines listed near the top of this thread. The gcc-gfortran install should no longer be needed because it's part of the vagrant script now.
from ambermini.
Any progress on automating this? If not, I will just upload the package that I already built.
from ambermini.
OK, I uploaded my new package to omnia, so I'm closing the issue now.
https://binstar.org/omnia/ambermini/files
from ambermini.
@kyleabeauchamp : Can you show me how you built this today? Hoping to automate this too.
from ambermini.
Sure. AFAIK, I believe this sequence of commands will finish the entire build chain:
git clone [email protected]:omnia-md/virtual-machines.git
cd virtual-machines/linux/
vagrant up
vagrant ssh
export PATH=$HOME/miniconda/bin:$PATH
git clone https://github.com/omnia-md/conda-recipes.git
cd conda-recipes
conda build ambermini
binstar upload -u omnia PATH_TO_OUTPUT/ambermini-14.0.1-0.tar.bz2 --force
# You can get the path to the output from reading the output of the conda build.
from ambermini.
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from ambermini.