Fedora 33 Gcc 11 (cmake, serial+openmp) builds fine. Built using:
./clean_build && ./configure_cmake.py --prefix
/home/droe/amber/GIT/test --source /home/droe/amber/GIT/amber20_src
--compiler GNU --openmp && make -j4 install
Almost all AT tests pass. However, there is an error when trying to
import pytraj. It seems that libcpptraj.so gets linked to the
libstdc++ from miniconda, and that requires a much higher version of
glibc (3.4.29) than what ships with fedora 33 (2.32). Note that this
happens with "configure" as well so it's not a cmake problem:
```
$ amber.python
Python 3.8.5 (default, Sep 4 2020, 07:30:14)
[GCC 7.3.0] :: Anaconda, Inc. on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import pytraj as pt
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/home/droe/amber/GIT/test/lib/python3.8/site-packages/./pytraj-2.0.6.dev0-py3.8-linux-x86_64.egg/pytraj/__init__.py",
line 24, in <module>
from .utils.misc import info
File "/home/droe/amber/GIT/test/lib/python3.8/site-packages/./pytraj-2.0.6.dev0-py3.8-linux-x86_64.egg/pytraj/utils/misc.py",
line 7, in <module>
from pytraj.core.c_options import set_world_silent
File "/home/droe/amber/GIT/test/lib/python3.8/site-packages/./pytraj-2.0.6.dev0-py3.8-linux-x86_64.egg/pytraj/core/__init__.py",
line 2, in <module>
from .topology_objects import Atom, Residue, Molecule
ImportError: /home/droe/amber/GIT/amber20_src/build/CMakeFiles/miniconda/install/lib/libstdc++.so.6:
version `GLIBCXX_3.4.29' not found (required by
/home/droe/amber/GIT/amber20_src/build/AmberTools/src/cpptraj/src/libcpptraj.so)
```
There is also an mmpbsa.py test failure that might be round-off:
```
possible FAILURE: check
/home/droe/amber/GIT/test///AmberTools/src/mm_pbsa/Examples/05_MMPBSA_Decomp_Residue/test_statistics.out.dif
/home/droe/amber/GIT/test/AmberTools/src/mm_pbsa/Examples/05_MMPBSA_Decomp_Residue
6c6
< 3 7 4.63 1.13 12.69 0.81
17.32 1.91 -3.33 0.41 -3.26 0.40
-6.59 0.47 8.88 1.61 -7.44 2.08
1.44 1.72 10.19 1.05 1.99 2.96 12.18
2.74 -4.34 1.06 -3.17 1.62 -7.50
1.08 0.02 0.01 0. 0. 0.02 0.01
-4.31 1.07 -3.17 1.62 -7.48 1.08
5.87 0.39 -1.17 1.35 4.70 1.72 -3.19
0.70 -0.59 0.74 -3.78 0.65 -3.17
0.71 -0.59 0.74 -3.76 0.66 7.01
0.62 1.41 2.29 8.42 2.49
> 3 7 4.63 1.13 12.69 0.81 17.32 1.91 -3.33 0.41 -3.26 0.40 -6.59 0.47 8.88 1.61 -7.44 2.08 1.44 1.72 10.19 1.05 1.99 2.96 12.18 2.74 -4.34 1.06 -3.17 1.62 -7.50 1.08 0.02 0.01 0. 0. 0.02 0.01 -4.31 1.07 -3.17 1.62 -7.48 1.08 5.87 0.39 -1.17 1.35 4.70 1.72 -3.19 0.70 -0.59 0.74 -3.78 0.65 -3.17 0.71 -0.59 0.74 -3.76 0.66 7.01 0.62 1.40 2.29 8.42 2.49
### Maximum absolute error in matching lines = 1.00e-02 at line 6 field 65
### Maximum relative error in matching lines = 7.14e-03 at line 6 field 65
```
-Dan
On Thu, May 20, 2021 at 4:06 PM Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
> Hi,
>
> Current master builds fine for me using cmake (serial + OpenMP) with
> gcc 10 (including readline-enabled cpptraj). Still need to run tests.
> Will test gcc11 next.
>
> -Dan
>
> On Thu, May 20, 2021 at 11:01 AM David A Case <david.case.rutgers.edu> wrote:
> >
> > Hi everyone:
> >
> > We think we have been able to squash a number of minor problems with
> > AmberTools21: getting readline support into cpptraj; fix python installation
> > problems; supporting gfortran11; fixing NAB compiles on some OSX
> > configurations. These have been merged to the master development branch.
> >
> > I'm hoping to get some tests of this before we push out updates to users.
> > So, it would be great if a few people (especially OSX users) could do the
> > following:
> >
> > cd amber20_src/build
> > ./clean_build
> > ./run_cmake
> > make install
> >
> > It's not really necessary to run all the tests, although you can if you
> > wish. I'm mainly interested to see if the build breaks on someone's
> > machine. And please try the following:
> >
> > $AMERHOME/bin/pdb4amber -h
> >
> > to see if you get the help prompt.
> >
> > Probably simplest to reply to amber-developers with results: brief reports
> > are best unless you are finding problems.
> >
> > ....thx...dac
> >
> >
> > _______________________________________________
> > AMBER-Developers mailing list
> > AMBER-Developers.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber-developers
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Received on Fri May 21 2021 - 07:30:02 PDT
