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genesis-release-r-ccs / genesis

Source, test set, and document for Molecular Dynamics software, GENESIS.
GNU Lesser General Public License v3.0
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Unable to install #1

Closed shuvadipkhanra closed 5 months ago

shuvadipkhanra commented 5 months ago

**During installation encountered by following issues.

Probably fortran issue @argument mismatch issue. how to resolve this problem?**

(base) shuvadip@shuvadip:~/Downloads/genesis-2.1.2$ ./configure --enable-single --enable-gpu 

24 bytes stack frame, 0 bytes spill stores, 0 bytes spill loads

ptxas info : Used 62 registers, 564 bytes cmem[0], 12 bytes cmem[2] ptxas info : Compiling entry function '_Z56kern_compute_energy_nonbond_table_linear_univ_energy_sumPdPKdiiii' for 'sm_62' ptxas info : Function properties for _Z56kern_compute_energy_nonbond_table_linear_univ_energy_sumPdPKdiiii 0 bytes stack frame, 0 bytes spill stores, 0 bytes spill loads ptxas info : Used 30 registers, 1280 bytes smem, 352 bytes cmem[0] ptxas info : Compiling entry function mpif90 -I. -I../../src -I../lib -O3 -ffast-math -march=native -ffree-line-length-none -fallow-argument-mismatch -fopenmp -c sp_enefunc_table.f90 mpif90 -I. -I../../src -I../lib -O3 -ffast-math -march=native -ffree-line-length-none -fallow-argument-mismatch -fopenmp -c sp_grest_energy.f90 mpif90 -I. -I../../src -I../lib -O3 -ffast-math -march=native -ffree-line-length-none -fallow-argument-mismatch -fopenmp -c sp_fep_energy.f90 mpif90 -I. -I../../src -I../lib -O3 -ffast-math -march=native -ffree-line-length-none -fallow-argument-mismatch -fopenmp -c sp_domain.f90 cpp -traditional-cpp -traditional -DHAVE_CONFIG_H sp_enefunc_charmm.fpp sp_enefunc_charmm.f90 mpif90 -I. -I../../src -I../lib -O3 -ffast-math -march=native -ffree-line-length-none -fallow-argument-mismatch -fopenmp -c sp_enefunc_charmm.f90 cpp -traditional-cpp -traditional -DHAVE_CONFIG_H sp_alchemy.fpp sp_alchemy.f90 mpif90 -I. -I../../src -I../lib -O3 -ffast-math -march=native -ffree-line-length-none -fallow-argument-mismatch -fopenmp -c sp_alchemy.f90 cpp -traditional-cpp -traditional -DHAVE_CONFIG_H sp_fep_topology.fpp sp_fep_topology.f90 mpif90 -I. -I../../src -I../lib -O3 -ffast-math -march=native -ffree-line-length-none -fallow-argument-mismatch -fopenmp -c sp_fep_topology.f90 ../lib/lib.a -fopenmp -llapack -lblas -L/usr/local/cuda-11.8/lib64 -lcudart -lstdc++ make[4]: Leaving directory '/home/shuvadip/Downloads/genesis-2.1.2/src/spdyn' make[3]: Leaving directory '/home/shuvadip/Downloads/genesis-2.1.2/src/spdyn' make[3]: Entering directory '/home/shuvadip/Downloads/genesis-2.1.2/src' make[3]: Leaving directory '/home/shuvadip/Downloads/genesis-2.1.2/src' make[2]: Leaving directory '/home/shuvadip/Downloads/genesis-2.1.2/src' make[1]: Leaving directory '/home/shuvadip/Downloads/genesis-2.1.2/src' make[1]: Entering directory '/home/shuvadip/Downloads/genesis-2.1.2' make[1]: Nothing to be done for 'all-am'. make[1]: Leaving directory '/home/shuvadip/Downloads/genesis-2.1.2'

chig commented 5 months ago

I could not tell what the problem was from the message you indicated. Could you share us the log files of configure and make? The config.log is located in the directory where you executed './configure'. As for log of make, please execute the following commands. make clean make > make.log 2>&1 Then, you can find 'make.log'. please do not do 'make -j n' at this time. The log will be difficult to understand.

shuvadipkhanra commented 5 months ago

config.log make.log Kindly fiend the attachments...

chig commented 5 months ago

Thanks. I check the log files. However, it looks OK while nvcc shows so many warnings. (Since your CUDA is new, so it warns against GENESIS' code for older cards, but there should be no problem.) Please execute 'make install', then you can find bin/spdyn in the directory.

shuvadipkhanra commented 5 months ago

ok sir.. doing it

shuvadipkhanra commented 5 months ago

(base) shuvadip@shuvadip:~/Downloads/genesis-2.1.2$ make install Making install in src make[1]: Entering directory '/home/shuvadip/Downloads/genesis-2.1.2/src' Making install in lib make[2]: Entering directory '/home/shuvadip/Downloads/genesis-2.1.2/src/lib' make[3]: Entering directory '/home/shuvadip/Downloads/genesis-2.1.2/src/lib' make[4]: Entering directory '/home/shuvadip/Downloads/genesis-2.1.2/src/lib' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/home/shuvadip/Downloads/genesis-2.1.2/src/lib' make[3]: Leaving directory '/home/shuvadip/Downloads/genesis-2.1.2/src/lib' make[2]: Leaving directory '/home/shuvadip/Downloads/genesis-2.1.2/src/lib' Making install in spdyn make[2]: Entering directory '/home/shuvadip/Downloads/genesis-2.1.2/src/spdyn' Making install in ../lib make[3]: Entering directory '/home/shuvadip/Downloads/genesis-2.1.2/src/lib' make[4]: Entering directory '/home/shuvadip/Downloads/genesis-2.1.2/src/lib' make[5]: Entering directory '/home/shuvadip/Downloads/genesis-2.1.2/src/lib' make[5]: Nothing to be done for 'install-exec-am'. make[5]: Nothing to be done for 'install-data-am'. make[5]: Leaving directory '/home/shuvadip/Downloads/genesis-2.1.2/src/lib' make[4]: Leaving directory '/home/shuvadip/Downloads/genesis-2.1.2/src/lib' make[3]: Leaving directory '/home/shuvadip/Downloads/genesis-2.1.2/src/lib' Making install in . make[3]: Entering directory '/home/shuvadip/Downloads/genesis-2.1.2/src/spdyn' make[4]: Entering directory '/home/shuvadip/Downloads/genesis-2.1.2/src/spdyn' /usr/bin/mkdir -p '/home/shuvadip/Downloads/genesis-2.1.2//bin' /usr/bin/install -c spdyn '/home/shuvadip/Downloads/genesis-2.1.2//bin' make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/home/shuvadip/Downloads/genesis-2.1.2/src/spdyn' make[3]: Leaving directory '/home/shuvadip/Downloads/genesis-2.1.2/src/spdyn' make[2]: Leaving directory '/home/shuvadip/Downloads/genesis-2.1.2/src/spdyn' make[2]: Entering directory '/home/shuvadip/Downloads/genesis-2.1.2/src' make[3]: Entering directory '/home/shuvadip/Downloads/genesis-2.1.2/src' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/home/shuvadip/Downloads/genesis-2.1.2/src' make[2]: Leaving directory '/home/shuvadip/Downloads/genesis-2.1.2/src' make[1]: Leaving directory '/home/shuvadip/Downloads/genesis-2.1.2/src' make[1]: Entering directory '/home/shuvadip/Downloads/genesis-2.1.2' make[2]: Entering directory '/home/shuvadip/Downloads/genesis-2.1.2' make[2]: Nothing to be done for 'install-exec-am'. make[2]: Nothing to be done for 'install-data-am'. make[2]: Leaving directory '/home/shuvadip/Downloads/genesis-2.1.2' make[1]: Leaving directory '/home/shuvadip/Downloads/genesis-2.1.2'

shuvadipkhanra commented 5 months ago

yes found bin folder

(base) shuvadip@shuvadip:~/Downloads/genesis-2.1.2/bin$ l spdyn* (base) shuvadip@shuvadip:~/Downloads/genesis-2.1.2/bin$ ./spdyn hwloc/linux: Ignoring PCI device with non-16bit domain. Pass --enable-32bits-pci-domain to configure to support such devices (warning: it would break the library ABI, don't enable unless really needed). hwloc/linux: Ignoring PCI device with non-16bit domain. Pass --enable-32bits-pci-domain to configure to support such devices (warning: it would break the library ABI, don't enable unless really needed).

normal usage

% mpirun -np XX ./spdyn INP

check control parameters of md

% ./spdyn -h ctrl md

check control parameters of min

% ./spdyn -h ctrl min

check control parameters of remd

% ./spdyn -h ctrl remd

check control parameters of rpath

% ./spdyn -h ctrl rpath

check all control parameters of md

% ./spdyn -h ctrl_all md

check all control parameters of min

% ./spdyn -h ctrl_all min

check all control parameters of remd

% ./spdyn -h ctrl_all remd

check all control parameters of rpath

% ./spdyn -h ctrl_all rpath

shuvadipkhanra commented 5 months ago

i am interested to calculate Absolute ligand binding profile. I have experience with gromacs but Charmm gui yet not support so interested to calculate MD and ABE calculation. Thus spdyn is sufficient for the same?

chig commented 5 months ago

I'm sorry that I'm not sure about it. Please check our tutorials in website or manual. https://www.r-ccs.riken.jp/labs/cbrt/tutorials2022/ This is where we accept questions/reports for the GENESIS code, so please check the website for instructions on how to use it.