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cluster:161 [2017/08/07 09:48]
hmeij07
cluster:161 [2020/07/16 13:16] (current)
hmeij07
Line 1: Line 1:
 \\ \\
 **[[cluster:0|Back]]** **[[cluster:0|Back]]**
 +
 +==== lammps-11Aug17 ====
 +
 +lammps-11Aug17 (n78)\\
 +and now lammps-22Aug18 (n33-n37)\\
 +and now lammps-5Jun19 (microway)\\
 +
 +Update: 
 +  * n78/gtx1080 lammps 11aug17 (centos7, mpich3/mpic++, cuda 8/sm_61, /usr/local)
 +      * [[cluster:164|GTX 1080 Ti]]
 +  * n37/k20 lammps 22aug18 (centos7, openmpi 1.8.4/mpic++, cuda 9.2/sm_35, /usr/local) 
 +      * [[cluster:173|K20 Redo Usage]]
 +  * n33/k20 lammps 11aug17 + 22aug18 (centos6, openmpi 1.8.4, cuda 5/sm35, /share/apps/CENTOS6)
 +      * this page
 +  * n33/k20 older lammps (centos6, mvapich, cuda 5/sm_??, /cm/shared/apps)
 +      * /home/hmeij/sharptail/run.gpu or gromacs.sub files
 +
 + --- //[[hmeij@wesleyan.edu|Henk]] 2018/09/20 09:30//
 +
 +<code>
 +N78
 +# devel packages for libjpeg, blas, lapack, boost
 +
 +which nvcc
 +export PATH=/usr/local/mpich-3.1.4/bin:$PATH
 +export LD_LIBRARY_PATH=/usr/local/mpich-3.1.4/lib:$LD_LIBRARY_PATH
 +which mpicxx
 +
 +# untar stable.gz
 +cd lib/gpu
 +vi Makefile.linux.double
 +# edits
 +CUDA_HOME = /usr/local/cuda
 +
 +# best fitting ARCH for GTX 1080 with CUDA 8+
 +CUDA_ARCH = -arch=sm_61
 +# best fitting ARCH for P100 with CUDA 8+
 +CUDA_ARCH = -arch=sm_60
 +# best fitting ARCH for RTX/T4 with CUDA 10+
 +CUDA_ARCH = -arch=sm_75
 +http://arnon.dk/matching-sm-architectures-arch-and-gencode-for-various-nvidia-cards/
 +
 +# generate DOUBLE_DOUBLE (case matters)
 +CUDA_PRECISION = -D_DOUBLE_DOUBLE
 +make -f Makefile.linux.double
 +ls -lrt
 +# new files: libgpu.a and Makefile.lammps
 +
 +cd ../../src/
 +vi MAKE/Makefile.mpi
 +# edits
 +LMP_INC =       -DLAMMPS_GZIP -DLAMMPS_MEMALIGN=64 -DLAMMPS_JPEG
 +JPG_INC =       -I/usr/include
 +JPG_PATH =      -L/usr/lib64
 +JPG_LIB =       -ljpeg
 +
 +
 +make purge
 +make yes-rigid
 +make yes-gpu
 +make yes-colloid
 +make yes-class2
 +make yes-kspace
 +make yes-misc
 +make yes-molecule
 +make yes-user-omp
 +make package-update
 +
 +which mpicxx
 +make mpi
 +mv lmp_mpi /usr/local/lammps-11Aug17/lmp_mpi-double-double-with-gpu[-rigid]
 +
 +# repeat from scratch for SINGLE_SINGLE and SINGLE_DOUBLE
 +# different makefiles same edits
 +
 +
 +</code>
  
 ==== Lammps CPU/GPU ==== ==== Lammps CPU/GPU ====
Line 17: Line 94:
 <code> <code>
  
-on n33, a gpu node+N33, a gpu node
  
-  mkdir /tmp/laamps; cd !$+  mkdir /tmp/lammps; cd !$
   gunzip lammps-stable.tar.gz    gunzip lammps-stable.tar.gz 
   tar xvf lammps-stable.tar    tar xvf lammps-stable.tar 
Line 51: Line 128:
    cd ..    cd ..
    #no cp MAKE/Makefile.serial MAKE/Makefile.serial_icc      #no cp MAKE/Makefile.serial MAKE/Makefile.serial_icc  
-   # edit MAKE/MAkefile.serial+    
 +   add compiler flag (centos7, 2020: -std=c++11) 
 +    
 +   # edit MAKE/Makefile.serial
    # leave gcc++  icc/icpc -DLAMMPS_JPEG for LMP_INC    # leave gcc++  icc/icpc -DLAMMPS_JPEG for LMP_INC
    # JPG_INC =   -I/usr/include    # JPG_INC =   -I/usr/include
Line 132: Line 212:
 # need both /cm/shared... and /cm/local ... # need both /cm/shared... and /cm/local ...
  
-# the malaysan approach also works, see install file+# the malaysian approach also works, see install file
  
  
Line 268: Line 348:
 # stage the data # stage the data
 scp -r ~/lammps/colloid-gpu/* . scp -r ~/lammps/colloid-gpu/* .
-# feed the wrapper+# feed the binary
 /share/apps/CENTOS6/lammps/31Mar17/lmp_mpi -h /share/apps/CENTOS6/lammps/31Mar17/lmp_mpi -h
 /share/apps/CENTOS6/lammps/31Mar17/lmp_mpi \ /share/apps/CENTOS6/lammps/31Mar17/lmp_mpi \
cluster/161.1502113728.txt.gz · Last modified: 2017/08/07 09:48 by hmeij07