Some fixes for cudaCoord (group-to-group)

plugins/cudaCoord/Readme.md

@@ -7,6 +7,42 @@ This is the optimized version of the lesson that I presented in the [plumed-scho
 The files `cudaHelpers.cuh` and `cudaHelpers.cu` contains a few support functions for helping in interfacing `PLMD::Vector` and `PLMD::Tensor` with Cuda's thrust,
 along with the reduction functions baked with Cuda's cub building blocks and their drivers.
 
+### Compile
+
+
+
+##### as developer
+
+With a ready to run plumed:
+  - `nvcc-MakeFile.sh`
+  - `make`
+
+In this way you do not need to recompile everithing if you change part of the sources
+
+you may need to specify the SM of your GPU by modifying the `Makefile`, for example with:
+
+```Makefile
+NVCCCFLAGS = -dc -dlto --gpu-architecture=sm_75 
+NVCCLDFLAGS = -shared -dlto --gpu-architecture=sm_75 
+```
+If you are using a T1000
+
+#### as a user
+
+Running `nvcc-mklib.sh` should be enought to get the `CudaCoordination.so`.
+
+you may need to uncomment and modifly the lines
+```bash
+#compile="$compile --gpu-architecture=sm_75 "
+#link_command="$link_command -shared -dlto --gpu-architecture=sm_75"
+```
+near the bottom of the script
+
+### How to tests
+
+ - `cd regtest; ln -s ../../../regtest/scripts .`
+ - `make check`
+
 ## Limitations
 
 `CUDACOORDINATION` and `CUDACOORDINATIONFLOAT` work more or less as the standard `COORDINATION`, except from:

plugins/cudaCoord/nvcc-mklib.sh

@@ -62,6 +62,13 @@ for opt in -f; do
   link_command=${link_command//${opt}/-Xcompiler ${opt}}
 done
 
+#this may be necessary for succesfully run on your GPU
+# search your GPU here https://developer.nvidia.com/cuda-gpus and specify sm_number
+# where "number" is the compute capability with no dots (the T1000 has CC of 7.5, so you write sm_75)
+
+#compile="$compile --gpu-architecture=sm_75 "
+#link_command="$link_command -shared -dlto --gpu-architecture=sm_75"
+
 eval "$compile" -o "$obj" "$file" && \
 eval "$compile" -o "ndReduction.o" "ndReduction.cu" && \
 eval "$link_command" -o "$lib" "ndReduction.o" "$obj"

plugins/cudaCoord/regtest/cudatestWB/rt-double-multiple-nopbc/plumed.dat

@@ -1,16 +1,16 @@
 LOAD FILE=../../../../CudaCoordination.so
-gpu: CUDACOORDINATION GROUPA=1-108,1-108 GROUPB=1-108,1-108  R_0=1 NOPBC
-gpu512: CUDACOORDINATION GROUPA=1-108,1-108 GROUPB=1-108,1-108  R_0=1 THREADS=512 NOPBC
-gpu256: CUDACOORDINATION GROUPA=1-108,1-108 GROUPB=1-108,1-108  R_0=1 THREADS=256 NOPBC
-gpu128: CUDACOORDINATION GROUPA=1-108,1-108 GROUPB=1-108,1-108  R_0=1 THREADS=128 NOPBC
-gpu64: CUDACOORDINATION GROUPA=1-108,1-108 GROUPB=1-108,1-108  R_0=1 THREADS=64 NOPBC
-cpu: COORDINATION GROUPA=1-108,1-108 GROUPB=1-108,1-108  R_0=1 NOPBC
+gpu:    CUDACOORDINATION GROUPA=108-1:-1,108-50:-1,1-49 GROUPB=1-108,1-108  R_0=1 NOPBC
+gpu512: CUDACOORDINATION GROUPA=108-1:-1,108-50:-1,1-49 GROUPB=1-108,1-108  R_0=1 THREADS=512 NOPBC
+gpu256: CUDACOORDINATION GROUPA=108-1:-1,108-50:-1,1-49 GROUPB=1-108,1-108  R_0=1 THREADS=256 NOPBC
+gpu128: CUDACOORDINATION GROUPA=108-1:-1,108-50:-1,1-49 GROUPB=1-108,1-108  R_0=1 THREADS=128 NOPBC
+gpu64:  CUDACOORDINATION GROUPA=108-1:-1,108-50:-1,1-49 GROUPB=1-108,1-108  R_0=1 THREADS=64 NOPBC
+cpu:        COORDINATION GROUPA=108-1:-1,108-50:-1,1-49 GROUPB=1-108,1-108  R_0=1 NOPBC
 
-diff: CUSTOM ARG=gpu,cpu FUNC=y-x PERIODIC=NO
+diff:    CUSTOM ARG=gpu,cpu    FUNC=y-x PERIODIC=NO
 diff512: CUSTOM ARG=gpu512,cpu FUNC=y-x PERIODIC=NO
 diff256: CUSTOM ARG=gpu256,cpu FUNC=y-x PERIODIC=NO
 diff128: CUSTOM ARG=gpu128,cpu FUNC=y-x PERIODIC=NO
-diff64: CUSTOM ARG=gpu64,cpu FUNC=y-x PERIODIC=NO
+diff64:  CUSTOM ARG=gpu64,cpu  FUNC=y-x PERIODIC=NO
 
 #PRINT ARG=gpu,cpu FILE=colvar FMT=%8.4f STRIDE=1
 PRINT ARG=diff FILE=colvar FMT=%8.4f STRIDE=1

plugins/cudaCoord/regtest/cudatestWB/rt-double-orthopbc-1-all/Makefile

@@ -0,0 +1 @@
+include ../../scripts/test.make

plugins/cudaCoord/regtest/cudatestWB/rt-double-orthopbc-1-all/colvar.reference

@@ -0,0 +1,11 @@
+#! FIELDS time diff
+ 0.000000  -0.0000
+ 1.000000   0.0000
+ 2.000000   0.0000
+ 3.000000   0.0000
+ 4.000000  -0.0000
+ 5.000000  -0.0000
+ 6.000000  -0.0000
+ 7.000000  -0.0000
+ 8.000000  -0.0000
+ 9.000000  -0.0000

plugins/cudaCoord/regtest/cudatestWB/rt-double-orthopbc-1-all/config

@@ -0,0 +1,11 @@
+type=driver
+# this is to test a different name
+arg="--plumed plumed.dat --ixyz traj-ortho.xyz"
+
+plumed_regtest_after() {
+  {
+    echo '#! FIELDS time parameter cpu-gpu'
+    awk 'NR>1{print $1, $2, $4-$3} ' <deriv
+  } >deriv_delta
+}
+extra_files="../../trajectories/traj-ortho.xyz"