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Pass on gpu options #193

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merged 5 commits into from
Aug 25, 2020
Merged

Pass on gpu options #193

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28d88e2
fix mixing of tabs and spaces
Aug 24, 2020
7bacdaf
pass on --no-gpu and --cuda--version
Aug 24, 2020
a3503bf
add flags to correct commad line
Aug 24, 2020
29099d3
Don't skip printing input variables
Aug 25, 2020
1be0a33
Removed comments put in for testing
Aug 25, 2020
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38 changes: 35 additions & 3 deletions DiffusionPreprocessing/DiffPreprocPipeline.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -175,6 +175,12 @@ PARAMETERs are: [ ] = optional; < > = user supplied value
eddy binary, the following sequence will work:

--extra-eddy-arg=-flag --extra-eddy-arg=value
[--no-gpu] If specified, use the non-GPU-enabled version of eddy.
Defaults to using the GPU-enabled version of eddy.
[--cuda-version=X.Y] If using the GPU-enabled version of eddy, then this
option can be used to specify which eddy_cuda binary
version to use. If specified, FSLDIR/bin/eddy_cudaX.Y
will be used.

[--combine-data-flag=<value>]
Specified value is passed as the CombineDataFlag value
Expand Down Expand Up @@ -214,12 +220,12 @@ EOF
# ${StudyFolder} Path to subject's data folder
# ${Subject} Subject ID
# ${PEdir} Phase Encoding Direction, 1=LR/RL, 2=AP/PA
# ${PosInputImages} @ symbol separated list of data with 'positive' phase
# ${PosInputImages} @ symbol separated list of data with 'positive' phase
# encoding direction
# ${NegInputImages} @ symbol separated lsit of data with 'negative' phase
# encoding direction
# ${echospacing} Echo spacing in msecs
# ${GdCoeffs} Path to file containing coefficients that describe
# ${GdCoeffs} Path to file containing coefficients that describe
# spatial variations of the scanner gradients. NONE
# if not available.
# ${DWIName} Name to give DWI output directories
Expand All @@ -230,9 +236,13 @@ EOF
# ${runcmd} Set to a user specifed command to use if user has
# requested that commands be echo'd (or printed)
# instead of actually executed. Otherwise, set to
# empty string.
# empty string.
# ${extra_eddy_args} Generic string of arguments to be passed to the
# eddy binary
# ${no_gpu} true if we should use the non-GPU-enabled version of eddy
# Anything else or unset means use the GPU-enabled version of eddy
# ${cuda_version} If using the GPU-enabled version, this value _may_ be
# given to specify the version of the CUDA libraries in use.
# ${CombineDataFlag} CombineDataFlag value to pass to
# DiffPreprocPipeline_PostEddy.sh script and
# subsequently to eddy_postproc.sh script
Expand All @@ -259,6 +269,8 @@ get_options() {
b0maxbval=${DEFAULT_B0_MAX_BVAL}
runcmd=""
extra_eddy_args=""
no_gpu=""
cuda_version=""
CombineDataFlag=1

# parse arguments
Expand Down Expand Up @@ -331,6 +343,14 @@ get_options() {
extra_eddy_args+=" ${extra_eddy_arg} "
index=$((index + 1))
;;
--no-gpu)
no_gpu="true"
index=$((index + 1))
;;
--cuda-version=*)
cuda_version=${argument#*=}
index=$((index + 1))
;;
--combine-data-flag=*)
CombineDataFlag=${argument#*=}
index=$((index + 1))
Expand Down Expand Up @@ -411,6 +431,10 @@ get_options() {
echo " SelectBestB0: ${SelectBestB0}"
fi
echo " extra_eddy_args: ${extra_eddy_args}"
if [ ! -z ${no_gpu} ]; then
echo " no_gpu: ${no_gpu}"
fi
echo " cuda-version: ${cuda_version}"
echo "-- ${g_script_name}: Specified Command-Line Parameters - End --"

if [ ! -z "${SelectBestB0}" ]; then
Expand Down Expand Up @@ -504,6 +528,14 @@ main() {
eddy_cmd+=" --dwiname=${DWIName} "
eddy_cmd+=" --printcom=${runcmd} "

if [ "${no_gpu}" == "true" ]; then
# default is to use the GPU-enabled version
eddy_cmd+=" --no-gpu "
else
if [ ! -z "${cuda_version}" ]; then
eddy_cmd+=" --cuda-version=${cuda_version}"
fi
fi
if [ ! -z "${extra_eddy_args}" ]; then
for extra_eddy_arg in ${extra_eddy_args}; do
eddy_cmd+=" --extra-eddy-arg=${extra_eddy_arg} "
Expand Down
4 changes: 3 additions & 1 deletion DiffusionPreprocessing/DiffPreprocPipeline_Eddy.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -379,7 +379,9 @@ get_options() {
echo " resamp_value: ${resamp_value}"
echo " ol_nstd_value: ${ol_nstd_value}"
echo " extra_eddy_args: ${extra_eddy_args}"
echo " no_gpu: ${no_gpu}"
if [ ! -z ${no_gpu} ]; then
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I think our convention in other scripts is to print argument values even if they are empty or used the default.

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Ok, I've adjusted this to print all argument values. To make the printed output more meaningful I set the default value from no_gpu (and SelectBestB0) to false rather than an empty string.

echo " no_gpu: ${no_gpu}"
fi
echo " cuda-version: ${cuda_version}"
echo "-- ${g_script_name}: Specified Command-Line Parameters - End --"
}
Expand Down