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GAMUS compilation issue
#37730 11/26/19 11:15 AM
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Dmitriy Offline OP
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Hi guys!

I have encountered a problem during compilation of charmm with GAMUS.

I have used the following string for compilation

./install.com gnu large gfortran x86_64 gamus

The output:
//-----------------------------------
~/charmm/source/gamus/gamus.F90:607.34:

use param_store, only: set_params
1
Error: Symbol 'set_params' referenced at (1) not found in module 'param_store'
make: *** [gamus.o] Error 1
//-------------------------------------

As i understand, the problem is not in linkage of LAPACK and BLAS. Something wrong with compilation.

Could you please help me?

Re: GAMUS compilation issue
Dmitriy #37731 11/26/19 11:47 AM
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The code is incorrect. Change set_params to set_param in gamus.F90.


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
Re: GAMUS compilation issue
lennart #37732 11/26/19 01:03 PM
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Dmitriy Offline OP
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Lennart, thank you for your prompt reply!

Yeap, now compilation is successful, but a have a lot of undefined references on a linkage stage concerning C++ structures.

For example,
undefined reference to `std::cout'
undefined reference to `std::string::append(std::string const&)'
undefined reference to `std::string::assign(std::string const&)'

As i understand I need to point out the C++ library explicitly, like -lstdc++ or somehow else.

Could you please tell me how can I show it via using install script?

Dmitriy

Dmitriy

Re: GAMUS compilation issue
Dmitriy #37733 11/26/19 03:15 PM
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I don't know which CHARMM version you have, but you should get the most recent version (free to download from http://charmm.chemistry.harvard.edu/charmm_lite.php) and use the cmake installation procedure.


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
Re: GAMUS compilation issue
Dmitriy #37735 11/26/19 06:40 PM
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I am attaching a patch to fix the install.com process. I will post this patch in the bugfixes topic too. The patch works for both c45a1 and c44b1.

Apply the patch to a fresh copy of the charmm source code. It includes fixes for source/gamus/gamus.F90, install.com and configure/cmake.

To apply the patch, change directory to the root of the charmm source code, and then issue the following command.

patch -p1 -i <full path to patch file>

Then you should be able to install charmm + gamus as usual with something like

./install.com gnu gamus

or

./configure --with-gamus

Attached Files
patch.txt (5.34 KB, 111 downloads)
Last edited by bucknerj; 11/26/19 09:30 PM.
Re: GAMUS compilation issue
bucknerj #37738 11/27/19 04:16 AM
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Dmitriy Offline OP
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Thank you for help, guys!

After applying fixes the building is successful.


Best regards,
Dmitriy


Moderated by  lennart, rmv 

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