compiling plumed 2.3.2 with libmatheval 1.1.11

[qingh...@gmail.com]

Hello,

I am struggling with compiling plumed 2.3.2 with libmatheval 1.1.11, I tried many times, but it is still not working.

Thanks to Davide Branduardi's previous post, I can compile libmatheval successfully without guile, using icc

Then, I set:

export LD_LIBRARY_PATH=/... path .../libmatheval1.1.11/lib/:$LD_LIBRARY_PATH
export LDFLAGS=-L/... path .../libmatheval1.1.11/lib
export CPPFLAGS=-I/... path .../libmatheval1.1.11/lib

PS: I also saw someone set the variables linked to libmatheval1.1.11/lib/.libs, I also tried that, also not working

then I go to plumed2.3.2, and do the configuration with

./configure CXX=mpiicpc CC=icc --prefix=/ ... path ... /

After the configuration, I add the flags to Makefile.conf:

DYNAMIC_LIBS= -lmatheval -L/pica/h1/qinghual/Programs/plumed2/libmatheval1.1.11/lib/
CPPFLAGS= -D__PLUMED_HAS_MATHEVAL=1 -I/pica/h1/qinghual/Programs/plumed2/libmatheval1.1.11/lib
LDFLAGS= -rdynamic /pica/h1/qinghual/Programs/plumed2/libmatheval1.1.11/lib/

then run make and make install, but I got the error like this:

~/libmatheval1.1.11/lib/libmatheval.so: undefined reference to `yywrap'


I googled, I found that this problem might come from flex (flex 2.5.37 was installed on the cluster ) , then I tried to compile libmatheval by adding a flag of "--noyywrap" to flex in the Makefile, as sugguested here: https://github.com/UWPRG/Plumed/blob/master/compile_plumed_gromacs_matheval.md

but I still got the same error

I even tried to install my own flex (flex 2.6.4 ), then install libmatheval, and then plumed, but it is still the same error I got.

As I read, the function of yywrap is not necessary for libmatheval, any suggestion on how to fix this problem? Thanks a lot!


All the best,
Qinghua

[qingh...@gmail.com]

By the way, I installed plumed 2.3.2 with libmatheval successfully on my local desktop, ubuntu 16.04, gcc 5.4.0 and openmpi 2.02 were used.

First, sudo apt-get install libmatheval-dev,

then I just go to plumed2.3.2:

./configure CXX=mpic++ --prefix=/  ... path .../
make -j 4
make install

it is successful. plumed detected libmatheval and -D__PLUMED_HAS_MATHEVAL=1 was added to Makefile.conf automatically.


All the best,
Qinghua

[qingh...@gmail.com]

Hello,

I switched to another cluster, and then I successfully installed plumed 2.3.2 with libmatheval 1.1.11, and later gromacs 2016.3 with plumed 2.3.2

I did the same as what I did on the other cluster, as post above, and this time everything went well without any error.
And I also did a test of MATHEVAL with plumed, it also worked well.

I guess the reason might be that flex 2.6.0 is installed on this cluster, while it is flex 2.5.37 on the other one (though I tried flex 2.6.4).


All the best,
Qinghua

[Flaviyan Jerome]

Hi,

I am facing a similar issue,

I tried multiple things with no avail. 

plume 2.3.2, mateval 1.1.11 and flex 2.6.4 

It would be better if the libmatheval can be packaged precompiled with plumed some how (like the molfile plugin)

any help here is appreciated. 

[Giovanni Bussi]

Hi,

including libmatheval in plumed (like the molfile plugin) would not solve the problem related to flex dependencies.

We are evaluating the possibility of including lepton library by Peter Eastman as an alternative to libmatheval directly in plumed source. There is an open issue here: https://github.com/plumed/plumed2/issues/244 It might require a few weeks for some of us to find the time to do it

Giovanni

--
You received this message because you are subscribed to the Google Groups "PLUMED users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to plumed-users+unsubscribe@googlegroups.com.
To post to this group, send email to plumed...@googlegroups.com.
Visit this group at https://groups.google.com/group/plumed-users.

To view this discussion on the web visit https://groups.google.com/d/msgid/plumed-users/2a1ec007-d158-4883-953a-6b61cda26006%40googlegroups.com.

For more options, visit https://groups.google.com/d/optout.

[Flaviyan Jerome]

Meanwhile, i followed the instructions at 

https://github.com/UWPRG/Plumed/blob/master/compile_plumed_gromacs_matheval.md, to compile the libmateval, 

After that I cofigured PLUMED with the following command 

./configure  --prefix=$HOME/local -enable-matheval=yes LDFLAGS="-L/path to libmatheval/lib" CPPFLAGS=-I/path to libmatheval/include LIBS="-lmatheval -lfl"

I have compiled PLUMED with libmatheval and works properly. 

To unsubscribe from this group and stop receiving emails from it, send an email to plumed-users...@googlegroups.com.

To post to this group, send email to plumed...@googlegroups.com.
Visit this group at https://groups.google.com/group/plumed-users.