Fixes

friofry · Jun 9, 2021 · 4f77873 · 4f77873
1 parent 6bc537e
commit 4f77873
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Showing 6 changed files with 11 additions and 11 deletions.
diff --git a/README.md b/README.md
@@ -48,7 +48,7 @@ The binary is in `motif_finder_gpu` folder
 1		Complementarity. 0 - forward strand. 1 - forward + reverse strand.
 8		Minimum score
 35		Maximum presence of motif for random reasons in the positive set of sequences [0-100]
-5		Minimum presence of motif for random reasons in a positive set of sequences [0-100]
+5		Minimum presence of motif in the positive set of sequences [0-100]
 test_12.fst		File with positive set of sequences
 0		0 - neutral frequencies, 1 - real nucleotide frequencies in the set of sequences [0, 1]
 1		Score type: 0 - chi-squared or 1 - binomial [0, 1]
@@ -59,7 +59,7 @@ test_12.fst		File with positive set of sequences
 0.fst		File with contrast set of sequences
 90		Maximum score in a contrast set of sequences
 0       deprecated
-0       Output results with Bonferroni correction [0, 1]
+0       Output results with Bonferroni correction. 0 - without correction , 1 - use correction [0, 1]
 ```
 
 ## Run motif_finder_gpu

diff --git a/gpu_lib/external_gpu_algorithm.cpp b/gpu_lib/external_gpu_algorithm.cpp
@@ -17,7 +17,7 @@ void external_gpu_algorithm(const std::vector<uint32_t> &motif_hashes,
                             const GpuCudaParams &params)
 {
     out_motif_weights.resize(motif_hashes.size(), 0);
-    uint32_t threads = (params.gpu_count > 0) ? params.gpu_count : std::thread::hardware_concurrency();
+    uint32_t threads = (params.gpu_count > 0) ? params.gpu_count : 1;
 
     SafeCounter motifs_counter(motif_hashes.size());
 

diff --git a/gpu_lib/gpu_cuda_params.h b/gpu_lib/gpu_cuda_params.h
@@ -6,7 +6,7 @@
 #include <config.h>
 
 struct GpuCudaParams {
-    uint32_t gpu_count { 0 };
+    uint32_t gpu_count { 1 };
     bool unified_memory {UNIFIED_MEMORY_SUPPORT};
     uint32_t motif_range_size {MOT_PER_CHUNK};
     uint32_t threads_per_block {THREADS_PER_BLOCK};

diff --git a/gpu_lib/internal_gpu_algorithm.cpp b/gpu_lib/internal_gpu_algorithm.cpp
@@ -16,7 +16,7 @@ void internal_gpu_algorithm(const SequenceHashes &sequence_hashes,
                             const GpuCudaParams &params)
 {
     out_motif_weights.resize(TOTAL_MOT, 0);
-    uint32_t threads = (params.gpu_count > 0) ? params.gpu_count : std::thread::hardware_concurrency();
+    uint32_t threads = (params.gpu_count > 0) ? params.gpu_count : 1;
 
     SafeCounter motifs_counter(TOTAL_MOT);
 

diff --git a/motif_finder_gpu/init.ini b/motif_finder_gpu/init.ini
@@ -1,7 +1,7 @@
 1		Complementarity. 0 - forward strand. 1 - forward + reverse strand.
 8		Minimum score
 35		Maximum presence of motif for random reasons in the positive set of sequences [0-100]
-5		Minimum presence of motif for random reasons in a positive set of sequences [0-100]
+5		Minimum presence of motif in the positive set of sequences [0-100]
 test_12.fst		File with positive set of sequences
 0		0 - neutral frequencies, 1 - real nucleotide frequencies in the set of sequences [0, 1]
 1		Score type: 0 - chi-squared or 1 - binomial [0, 1]
@@ -12,4 +12,4 @@ test_12.fst		File with positive set of sequences
 0.fst		File with contrast set of sequences
 90		Maximum score in a contrast set of sequences
 0       deprecated
-0       Output results with Bonferroni correction [0, 1]
+0       Output results with Bonferroni correction. 0 - without correction , 1 - use correction [0, 1]
diff --git a/running_on_nusc_cluster.md b/running_on_nusc_cluster.md
@@ -12,15 +12,15 @@ qsub -I -l walltime=00:30:00 -l select=1:ngpus=4:ncpus=12:mem=40gb -q a6500g10q@
 ```
 3. Unpack the sources:
 ```shell
-unzip v1.0.zip -d .
+unzip motif_finder_cuda-1.0.zip -d .
 ```
 4. Navigate to the sourcedir:
 ```shell
-cd motif_finder_cuda
+cd motif_finder_cuda-1.0
 ```
 5. Create build dir and navigate to it:
 ```shell
-mkdir biuld
+mkdir build
 cd build
 ```
 6. Configure project:
@@ -30,7 +30,7 @@ cd build
 
 7. Build:
 ```shell
-/cmake-3.20.3-linux-x86_64/bin/cmake --build . -j
+~/cmake-3.20.3-linux-x86_64/bin/cmake --build . -j
 ```
 
 8. Run: