| ... | @@ -186,10 +186,142 @@ E_pairext: NEW= 0 OLD= 0 DIFF= 0 CONVS |
... | @@ -186,10 +186,142 @@ E_pairext: NEW= 0 OLD= 0 DIFF= 0 CONVS |
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# WRITING CHECKPOINT FILE `test_checkpoint.dat`
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# WRITING CHECKPOINT FILE `test_checkpoint.dat`
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# TIMING rt_tot= 0.51: rt_zheev= 0.03[ 5.56%] rt_dens= 0.00[ 0.72%] rt_pot= 0.00[ 0.14%] rt_me= 0.00[ 0.06%] rt_redistrib= 0.00[ 0.31%] rt_other= 0.48[93.21%]
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# TIMING rt_tot= 0.51: rt_zheev= 0.03[ 5.56%] rt_dens= 0.00[ 0.72%] rt_pot= 0.00[ 0.14%] rt_me= 0.00[ 0.06%] rt_redistrib= 0.00[ 0.31%] rt_other= 0.48[93.21%]
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# ALGORITHM CONVERGED!
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# ALGORITHM CONVERGED!
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```
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```
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# Step 5: Setting templates for `td` codes
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# Step 5: Setting templates for `td` codes
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The same operations were applied to `td-project-template` and `td-testcase-uniform` folders. The following files were modified to the form as presented below.
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### env.sh
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```bash
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# source env.sh
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module load openmpi/3.1.4_gcc620
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module unload cudatoolkit
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module load cuda/11.2.1_460.32.03
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module list
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cat $WSLDA/VERSION.h
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```
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### Makefile
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```bash
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# LOAD MODULES BEFORE COMPILATION
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#
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# module load openmpi/3.1.4_gcc620
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# module unload cudatoolkit
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# module load cuda/11.2.1_460.32.03
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# COMPILERS
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CXX=mpicc
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NVCC=nvcc
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PYTHON=python
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# DIRECTORY SETTINGS (must end with /)
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# W-SLDA instalation folder (for read only)
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WSLDADIR=/mnt/storage_2/project_data/grant_518/wslda/
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# folder where temporarry files will be stored (will be created automatically)
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OBJDIR=./obj/
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# folder where executable binary will be placed (will be created automatically)
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BINDIR=./
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# COMPILER FLAGS & LIBRARIES
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# C compiler flags
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CFLAGS= -std=gnu99 -O3
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# CUDA compiler flags
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NVCCFLAGS = -arch sm_60 -O3
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# prescription how to link with: FFTW, CUDA
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LIBS=-lcudart -lcufft -lfftw3 -lm
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# ----- DO NOT MODIFY -----
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include $(WSLDADIR)hpc-engine/mk.td
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```
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### job.sh
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```bash
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#!/bin/bash -l
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#SBATCH -J test # name that will be displayed in queue system
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#SBATCH --output="test.out" # stdout will be saved here
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#SBATCH -N 1 # here set number of nodes
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#SBATCH -n 32 # must be N*32
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#SBATCH --mem-per-cpu=2GB
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#SBATCH --gpus-per-node=8 # use 8 if you want to use Altair nodes
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#SBATCH --time=24:00:00 # here set walltime hh:mm:ss
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#SBATCH --mail-type=BEGIN,END,FAIL # notifications for job started, done & fail
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#SBATCH --mail-user=your@email # send-to address
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#SBATCH -p tesla
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## ------ QUEUE SYSTEM ------
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## For submission use:
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## sbatch job.sh
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## For checking status use:
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## squeue
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## To kill job use:
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## scancel pid
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##
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## ------ COMPUTATION -------
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## For computation it is recomended to use location:
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## cd ~/grant_518/scratch/
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cd $SLURM_SUBMIT_DIR
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source ./env.sh
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## NOTE: YOU MUST ASSURE: -np=N*gpus-per-node
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## -npernode=gpus-per-node
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mpirun -np 8 -npernode 8 ./td-wslda-2d input.txt
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```
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### input.txt
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The `job.sh` script is configured to send the code to standard GPU nodes, with `gpus-per-node=8`. Thus, one needs to set the correct value of `gpuspernode` in template of input file.
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```bash
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gpuspernode 8 # must be equal gpus-per-node provided in the job script, 8 for Altair nodes
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```
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## Testing `td` codes
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For testing, it is recommended to use `td-testcase-uniform`.
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```
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# Use scratch area for tests
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gabrielw@eagle:~$ cd grant_518/scratch/
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gabrielw@eagle:~/grant_518/scratch$ cp -r $WSLDA/td-testcase-uniform .
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gabrielw@eagle:~/grant_518/scratch$ cd td-testcase-uniform/
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gabrielw@e1296:/mnt/storage_2/scratch/grant_518/td-testcase-uniform$ ls
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env.sh input.txt job.sh logger.h Makefile predefines.h problem-definition.h README.txt
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# Compile codes
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gabrielw@eagle:~/grant_518/scratch/td-testcase-uniform$ srun --pty -n 1 /bin/bash
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gabrielw@e1296:/mnt/storage_2/scratch/grant_518/td-testcase-uniform$ source env.sh
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openmpi/3.1.4_gcc620 load complete.
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cuda/11.2.1_460.32.03 load complete.
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Currently Loaded Modulefiles:
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1) gmp/5.1.3(default) 2) mpfr/3.1.2(default) 3) libmpc/1.0.1(default) 4) gcc/6.2.0 5) openmpi/3.1.4_gcc620 6) cuda/11.2.1_460.32.03
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#define CODE "W-SLDA-TOOLKIT"
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#define VERSION "2021.09.05"
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gabrielw@e1296:~/grant_518/scratch/td-testcase-uniform$ make
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mkdir -p ./obj/
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mkdir -p ./
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mpicc -std=gnu99 -O3 -I/mnt/storage_2/project_data/grant_518/wslda/hpc-engine/ -I/mnt/storage_2/project_data/grant_518/wslda/lib/wdata/c/ -I/mnt/storage_2/project_data/grant_518/wslda/lib/wderiv/c/ -I/mnt/storage_2/project_data/grant_518/wslda/lib/winterp/c/ -I./ -DTDWSLDA -DCODEDIM=1 -c -o obj/ccpca.o /mnt/storage_2/project_data/grant_518/wslda/hpc-engine/ccpca.c
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# ...
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gabrielw@e1296:~/grant_518/scratch/td-testcase-uniform$ exit
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# submit the job and wait till it executes
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gabrielw@eagle:~/grant_518/scratch/td-testcase-uniform$ sbatch job.sh
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Submitted batch job 19731598
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# check is files were produced...
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gabrielw@eagle:~/grant_518/scratch/td-testcase-uniform$ ls
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env.sh logger.h predefines.h td-wslda-1d test test_input.txt test_logger.h test_problem-definition.h test.stdout
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input.txt Makefile problem-definition.h td-wslda-2d test_check.stamp test_j_a.wdat test.out test_rho_a.wdat test.wlog
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job.sh obj README.txt td-wslda-3d test_delta.wdat test_j_b.wdat test_predefines.h test_rho_b.wdat test.wtxt
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TODO |
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# ... and if the code was producing results - all numbers should be the same if everything went ok.
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\ No newline at end of file |
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gabrielw@eagle:~/grant_518/scratch/td-testcase-uniform$ tail test.stdout
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0.3500 17.00000061 17.99999904 34.99999965 0.43917132 1.91518974 -0.52650127 -0.94951715 0.00000000 0.00000000 0.00000000 0.00000000 -0.00000000 -0.00000000 0.25
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0.7000 17.00000061 17.99999904 34.99999965 0.43917132 1.91518974 -0.52650127 -0.94951715 0.00000000 0.00000000 0.00000000 0.00000000 -0.00000000 0.00000000 0.21
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1.0500 17.00000061 17.99999904 34.99999965 0.43917132 1.91518974 -0.52650127 -0.94951715 0.00000000 0.00000000 0.00000000 0.00000000 -0.00000000 -0.00000000 0.21
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1.4000 17.00000061 17.99999904 34.99999965 0.43917132 1.91518974 -0.52650127 -0.94951716 0.00000000 0.00000000 0.00000000 0.00000000 -0.00000000 -0.00000000 0.21
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1.7500 17.00000061 17.99999904 34.99999965 0.43917132 1.91518974 -0.52650127 -0.94951716 0.00000000 0.00000000 0.00000000 0.00000000 -0.00000000 -0.00000000 0.21
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2.1000 17.00000061 17.99999904 34.99999965 0.43917132 1.91518974 -0.52650127 -0.94951716 0.00000000 0.00000000 0.00000000 0.00000000 -0.00000000 0.00000000 0.21
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2.4500 17.00000061 17.99999904 34.99999965 0.43917132 1.91518974 -0.52650127 -0.94951716 0.00000000 0.00000000 0.00000000 0.00000000 -0.00000000 0.00000000 0.21
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2.8000 17.00000061 17.99999904 34.99999965 0.43917132 1.91518974 -0.52650127 -0.94951716 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.21
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3.1500 17.00000061 17.99999904 34.99999965 0.43917132 1.91518974 -0.52650127 -0.94951716 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.21
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3.5000 17.00000061 17.99999904 34.99999965 0.43917132 1.91518974 -0.52650127 -0.94951716 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.21
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``` |
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\ No newline at end of file |
