CP2K-3_0 with Plumed-2.2.0 installation problem

[tarak karmakar]

Dear All, 

I have successfully installed Plumed-2.2.0 in my system. Now, my next task is to patch it with CP2K-3_0. I followed the following steps,

1) added -D__PLUMED2 in DFLAGS, 

2) added the following two lines in 'Linux-x86-64-intel-mic.popt' file,

         include /home/tarak/software/plumed-2/lib/plumed/src/lib/Plumed.inc

         EXTERNAL_OBJECTS=$(PLUMED_STATIC_DEPENDENCIES)

2) make -j 4 ARCH=Linux-x86-64-intel-mic VERSION=popt

Whiling doing so, I encountered the following error,

-----------------------------------------------------------------------------------------------------------------

/home/tarak/software/plumed-2/lib/plumed/obj/PlumedStatic.o:(.data+0x0): undefined reference to `plumedmain_create'

/home/tarak/software/plumed-2/lib/plumed/obj/PlumedStatic.o:(.data+0x8): undefined reference to `plumedmain_cmd'

/home/tarak/software/plumed-2/lib/plumed/obj/PlumedStatic.o:(.data+0x10): undefined reference to `plumedmain_finalize'

make[3]: *** [/home/tarak/software/cp2k-3.0/exe/Linux-x86-64-intel-mic/graph.popt] Error 1

make[3]: *** Waiting for unfinished jobs....

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

make[1]: *** [popt] Error 2

make: *** [all] Error 2

-----------------------------------------------------------------------------------------------------------------

I would appreciate any suggestion.

Regards,

Tarak

[Giovanni Bussi]

Hi,

I think it is a small bug that we (in this case, I) introduced in the upgrade to plumed 2.2. I will fix it asap in the plumed repository. Meanwhile:

open /home/tarak/software/plumed-2/lib/plumed/src/lib/Plumed.inc

look for a line that looks like:

PLUMED_STATIC_LOAD= ... list of objects ... ... list of options ...

then edit the variable PLUMED_STATIC_DEPENDENCIES so that it is equal to the same list of objects.

In my case:

*** before correction:

PLUMED_RUNTIME_LOAD= "/Users/bussi/test-install-plumed/lib/plumed/obj/Plumed.o" -ldl

PLUMED_STATIC_LOAD= "/Users/bussi/test-install-plumed/lib/plumed/obj/kernel.o" "/Users/bussi/test-install-plumed/lib/plumed/obj/PlumedStatic.o" -ldl  -lstdc++ -lxdrfile -lgsl -lgslcblas -lz -lmatheval -ldl -lmolfile_plugin -llapack -lblas

PLUMED_SHARED_LOAD= "/Users/bussi/test-install-plumed/lib/libplumed.dylib" -ldl

PLUMED_RUNTIME_DEPENDENCIES=

PLUMED_STATIC_DEPENDENCIES= "/Users/bussi/test-install-plumed/lib/plumed/obj/PlumedStatic.o"

PLUMED_SHARED_DEPENDENCIES= "/Users/bussi/test-install-plumed/lib/libplumed.dylib"

*** after correction:

PLUMED_RUNTIME_LOAD= "/Users/bussi/test-install-plumed/lib/plumed/obj/Plumed.o" -ldl

PLUMED_STATIC_LOAD= "/Users/bussi/test-install-plumed/lib/plumed/obj/kernel.o" "/Users/bussi/test-install-plumed/lib/plumed/obj/PlumedStatic.o" -ldl  -lstdc++ -lxdrfile -lgsl -lgslcblas -lz -lmatheval -ldl -lmolfile_plugin -llapack -lblas

PLUMED_SHARED_LOAD= "/Users/bussi/test-install-plumed/lib/libplumed.dylib" -ldl

PLUMED_RUNTIME_DEPENDENCIES=

PLUMED_STATIC_DEPENDENCIES= "/Users/bussi/test-install-plumed/lib/plumed/obj/kernel.o" "/Users/bussi/test-install-plumed/lib/plumed/obj/PlumedStatic.o"

PLUMED_SHARED_DEPENDENCIES= "/Users/bussi/test-install-plumed/lib/libplumed.dylib"

Let us know if this fixes your issue.

Many thanks!

Giovanni

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[tarak karmakar]

Dear Giovanni, 

Thanks for looking at my problem. Yes, I modified the Plumed.inc file according to your suggestion. But now, I encountered another problem related to the metadynamics.F code,

-------------------------------------------------------------------------------------------------------------------------------------------------------------------

/home/tarak/software/cp2k-3.0/src/metadynamics.F(17): error #6580: Name in only-list does not exist.   [PBC_CP2K_PLUMED_GETSET_CELL]

                                             pbc_cp2k_plumed_getset_cell

---------------------------------------------^

/home/tarak/software/cp2k-3.0/src/metadynamics.F(123): error #6632: Keyword arguments are invalid without an explicit interface.   [SET]

    CALL pbc_cp2k_plumed_getset_cell (cell, set=.TRUE.) !Store the cell pointer for later use.

--------------------------------------------^

compilation aborted for /home/tarak/software/cp2k-3.0/src/metadynamics.F (code 1)

make[3]: *** [metadynamics.o] Error 1

make[3]: *** Waiting for unfinished jobs....

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

make[1]: *** [popt] Error 2

make: *** [all] Error 2

--------------------------------------------------------------------------------------------------------------------------------------------------------------------

Regards,

Tarak

To view this discussion on the web visit https://groups.google.com/d/msgid/plumed-users/CAPLm8ZKGr51Z%2Bd%2BUUZOeVML1VU8F7q7Uwo_R%2BeX9PUt2g7Szgw%40mail.gmail.com.

[Giovanni Bussi]

This is a bit surprising, I thought at the first round you were able to compile all the CP2K object files.

Anyway, this question is more for the CP2K mailing list.

Thanks!

Giovanni

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[tarak karmakar]

Hi Giovanni,

Yes, indeed. I could compile CP2K independently, generate the executable, and run a test job. The job is getting aborted at the free energy (metadynamics) step stating that CP2K is not installed with PLUMED. 

Still checking some of the libraries or linking issues. 

Anyway, thanks for your help. I will give another try after sometime, and let you know if I can successfully install it.  

Regards,

Tarak

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--

Tarak Karmakar
Molecular Simulation Lab.
Chemistry and Physics of Materials Unit
Jawaharlal Nehru Centre for Advanced Scientific Research
Jakkur P. O.
Bangalore - 560 064
Karnataka, INDIA
Ph. (lab) : +91-80-22082809