Removed logging output

plugins/amoeba/platforms/cuda/src/kernels/kCalculateAmoebaCudaElectrostatic.cu

@@ -777,9 +777,11 @@ void cudaComputeAmoebaElectrostatic( amoebaGpuContext amoebaGpu )
 
     if (gpu->bOutputBufferPerWarp){
 
+#ifdef AMOEBA_DEBUG
         (void) fprintf( amoebaGpu->log, "kCalculateAmoebaCudaElectrostaticN2Forces warp:  numBlocks=%u numThreads=%u bufferPerWarp=%u atm=%lu shrd=%lu ixnCt=%lu workUnits=%u\n",
                         amoebaGpu->nonbondBlocks, threadsPerBlock, amoebaGpu->bOutputBufferPerWarp,
                         sizeof(ElectrostaticParticle), sizeof(ElectrostaticParticle)*threadsPerBlock, (*gpu->psInteractionCount)[0], gpu->sim.workUnits ); (void) fflush( amoebaGpu->log );
+#endif
 
 
         kCalculateAmoebaCudaElectrostaticN2ByWarpForces_kernel<<<amoebaGpu->nonbondBlocks, threadsPerBlock, sizeof(ElectrostaticParticle)*threadsPerBlock>>>(

plugins/amoeba/platforms/cuda/src/kernels/kCalculateAmoebaCudaFixedEAndGkFields.cu

@@ -411,7 +411,6 @@ void cudaComputeAmoebaFixedEAndGkFields( amoebaGpuContext amoebaGpu )
     kClearFields_3( amoebaGpu, 3 );
 
     if (gpu->bOutputBufferPerWarp){
-        (void) fprintf( amoebaGpu->log, "N2 warp\n" );
         kCalculateAmoebaFixedEAndGkFieldN2ByWarp_kernel<<<amoebaGpu->nonbondBlocks, threadsPerBlock, sizeof(FixedFieldParticle)*threadsPerBlock>>>(
                                                                            amoebaGpu->psWorkUnit->_pDevData,
                                                                            gpu->psPosq4->_pDevData,

plugins/amoeba/platforms/cuda/src/kernels/kCalculateAmoebaCudaKirkwood.cu

@@ -1893,14 +1893,16 @@ void kCalculateAmoebaKirkwood( amoebaGpuContext amoebaGpu )
         //unsigned int eDiffhreadsPerBlock            = getThreadsPerBlock( amoebaGpu, sizeof(KirkwoodEDiffParticle));
         //unsigned int maxThreadsPerBlock             = threadsPerBlock> eDiffhreadsPerBlock ? threadsPerBlock : eDiffhreadsPerBlock;
 
+#ifdef AMOEBA_DEBUG
         if( amoebaGpu->log ){
-
             (void) fprintf( amoebaGpu->log, "kCalculateAmoebaCudaKirkwood: blcks=%u tds=%u %u bPrWrp=%u atm=%lu shrd=%lu ixnCt=%lu workUnits=%u\n",
                             amoebaGpu->nonbondBlocks, threadsPerBlock, maxThreads, amoebaGpu->bOutputBufferPerWarp,
                             sizeof(KirkwoodParticle), sizeof(KirkwoodParticle)*threadsPerBlock,
                             (*gpu->psInteractionCount)[0], gpu->sim.workUnits );
             (void) fflush( amoebaGpu->log );
         }
+#endif
+
     }
 
     kClearFields_1( amoebaGpu );

plugins/amoeba/platforms/cuda/src/kernels/kCalculateAmoebaCudaLocalForces.cu

@@ -1626,6 +1626,7 @@ void kCalculateAmoebaLocalForces_kernel()
 void kCalculateAmoebaLocalForces(amoebaGpuContext gpu)
 {
    
+#ifdef AMOEBA_DEBUG
     if( gpu->log ){
         static int call = 1;
         if( call == 0 ){
@@ -1634,6 +1635,7 @@ void kCalculateAmoebaLocalForces(amoebaGpuContext gpu)
             call++;
         }
     }
+#endif
     kCalculateAmoebaLocalForces_kernel<<<gpu->gpuContext->sim.blocks, gpu->gpuContext->sim.localForces_threads_per_block>>>();
 
     LAUNCHERROR("kCalculateAmoebaLocalForces");

plugins/amoeba/platforms/cuda/src/kernels/kCalculateAmoebaCudaMapTorques.cu

@@ -701,7 +701,7 @@ void cudaComputeAmoebaMapTorques( amoebaGpuContext amoebaGpu, CUDAStream<float>*
     // check that BLOCK_SIZE >= amoebaGpu->maxMapTorqueDifference
 
     if( amoebaGpu->maxMapTorqueDifference > BLOCK_SIZE ){
-        (void) fprintf( amoebaGpu->log, "cudaComputeAmoebaMapTorques: block size (%d) in amoebaMapTorqueReduce_kernel is too small ( > %d)! -- aborting.\n"
+        (void) fprintf( stderr, "cudaComputeAmoebaMapTorques: block size (%d) in amoebaMapTorqueReduce_kernel is too small ( > %d)! -- aborting.\n"
                         "This is likely due to the presence of disulfide bond or other bond between atoms whose indices is greater than %d; this limitation will be removed w/ the next software update.\n",
                         BLOCK_SIZE, amoebaGpu->maxMapTorqueDifference, BLOCK_SIZE );
         exit(-1);  
@@ -872,7 +872,7 @@ void cudaComputeAmoebaMapTorquesAndAddTotalForce( amoebaGpuContext amoebaGpu,
     // check that BLOCK_SIZE >= amoebaGpu->maxMapTorqueDifference
 
     if( amoebaGpu->maxMapTorqueDifference > BLOCK_SIZE ){
-        (void) fprintf( amoebaGpu->log, "cudaComputeAmoebaMapTorquesAndAddTotalForce: block size (%d) in amoebaMapTorqueReduce_kernel is too small ( > %d)! -- aborting.\n"
+        (void) fprintf( stderr, "cudaComputeAmoebaMapTorquesAndAddTotalForce: block size (%d) in amoebaMapTorqueReduce_kernel is too small ( > %d)! -- aborting.\n"
                         "This is likely due to the presence of disulfide bond or other bond between atoms whose indices is greater than %d; this limitation will be removed w/ the next software update.\n",
                         BLOCK_SIZE, amoebaGpu->maxMapTorqueDifference, BLOCK_SIZE );
         exit(-1);  
@@ -1075,7 +1075,7 @@ void cudaComputeAmoebaMapTorquesAndAddTotalForce2( amoebaGpuContext amoebaGpu,
     // check that BLOCK_SIZE >= amoebaGpu->maxMapTorqueDifference
 
     if( amoebaGpu->maxMapTorqueDifference > BLOCK_SIZE ){
-        (void) fprintf( amoebaGpu->log, "cudaComputeAmoebaMapTorquesAndAddTotalForce2: block size (%d) in amoebaMapTorqueReduce_kernel is too small ( > %d)! -- aborting.\n"
+        (void) fprintf( stderr, "cudaComputeAmoebaMapTorquesAndAddTotalForce2: block size (%d) in amoebaMapTorqueReduce_kernel is too small ( > %d)! -- aborting.\n"
                         "This is likely due to the presence of disulfide bond or other bond between atoms whose indices is greater than %d; this limitation will be removed w/ the next software update.\n",
                         BLOCK_SIZE, amoebaGpu->maxMapTorqueDifference, BLOCK_SIZE );
         exit(-1);

plugins/amoeba/platforms/cuda/src/kernels/kCalculateAmoebaCudaPmeDirectElectrostatic.cu

@@ -1392,6 +1392,7 @@ extern double kReduceEnergy(  gpuContext gpu);
 void cudaComputeAmoebaPmeElectrostatic( amoebaGpuContext amoebaGpu )
 {
 
+#ifdef AMOEBA_DEBUG
     if( 0 ){
         gpuContext gpu = amoebaGpu->gpuContext;
         std::vector<int> fileId;
@@ -1441,7 +1442,9 @@ void cudaComputeAmoebaPmeElectrostatic( amoebaGpuContext amoebaGpu )
         //zeroForce( amoebaGpu );
         exit(0);
     }
+#endif
 
+#ifdef AMOEBA_DEBUG
     if( 0 ){
         gpuContext gpu = amoebaGpu->gpuContext;
         std::vector<int> fileId;
@@ -1476,6 +1479,7 @@ void cudaComputeAmoebaPmeElectrostatic( amoebaGpuContext amoebaGpu )
         cudaLoadCudaFloatArray( gpu->natoms,  3, amoebaGpu->psForce,      outputVector, gpu->psAtomIndex->_pSysData, 1.0f );
         cudaWriteVectorOfDoubleVectorsToFile( "CudaPrePmeForce", fileId, outputVector );
     }
+#endif
 
     cudaComputeAmoebaPmeDirectElectrostatic( amoebaGpu );
     kCalculateAmoebaPMEInducedDipoleForces( amoebaGpu );

plugins/amoeba/platforms/cuda/src/kernels/kCalculateAmoebaCudaPmeMutualInducedField.cu

@@ -769,16 +769,16 @@ void) fflush( amoebaGpu->log );
                         amoebaGpu->psCurrentEpsilon->_pSysData[1], 
                         amoebaGpu->psCurrentEpsilon->_pSysData[2], done );
         (void) fflush( amoebaGpu->log );
+
 #endif
 
         // exit if nan
 
         if( 0 && amoebaGpu->mutualInducedCurrentEpsilon != amoebaGpu->mutualInducedCurrentEpsilon ){
-            (void) fprintf( amoebaGpu->log, "PME MI iteration=%3d eps is nan -- exiting.\n", iteration );
+            (void) fprintf( stderr, "PME MI iteration=%3d eps is nan -- exiting.\n", iteration );
             exit(0);
         }
 
-
         iteration++;
     }
 

plugins/amoeba/platforms/cuda/src/kernels/kCalculateAmoebaCudaRotateFrame.cu

@@ -605,8 +605,8 @@ void kCalculateAmoebaMultipoleForces(amoebaGpuContext amoebaGpu, bool hasAmoebaG
     // check if induce dipole calculation converged -- abort if it did not
 
     if( amoebaGpu->mutualInducedDone == 0 ){
-       (void) fprintf( amoebaGpu->log, "%s induced dipole calculation did not converge -- aborting!\n", methodName.c_str() );
-       (void) fflush( amoebaGpu->log );
+       (void) fprintf( stderr, "%s induced dipole calculation did not converge -- aborting!\n", methodName.c_str() );
+       (void) fflush( stderr );
        exit(-1);
     }
 

plugins/amoeba/platforms/cuda/src/kernels/kCalculateAmoebaCudaVdw14_7.cu

@@ -583,6 +583,7 @@ void kCalculateAmoebaVdw14_7Forces( amoebaGpuContext amoebaGpu, int applyCutoff
                     sizeof(unsigned int)*gpu->sim.nonbond_threads_per_block>>>(gpu->sim.pInteractingWorkUnit);
         LAUNCHERROR("kFindInteractionsWithinBlocksVdwPeriodic");
 
+#ifdef AMOEBA_DEBUG
         if( 0 ){  
             gpu->psInteractionCount->Download();
             gpu->psInteractingWorkUnit->Download();
@@ -605,6 +606,7 @@ void kCalculateAmoebaVdw14_7Forces( amoebaGpuContext amoebaGpu, int applyCutoff
             }    
                 (void) fflush( amoebaGpu->log );
         }
+#endif
 
         if (gpu->bOutputBufferPerWarp){
             kCalculateAmoebaVdw14_7CutoffByWarp_kernel<<<amoebaGpu->nonbondBlocks, threadsPerBlock, sizeof(Vdw14_7Particle)*threadsPerBlock>>>(

plugins/amoeba/platforms/cuda/src/kernels/kCalculateAmoebaCudaWcaDispersion.cu

@@ -30,10 +30,6 @@ void GetCalculateAmoebaCudaWcaDispersionSim(amoebaGpuContext amoebaGpu)
     cudaError_t status;
     gpuContext gpu = amoebaGpu->gpuContext;
     status = cudaMemcpyFromSymbol(&gpu->sim, cSim, sizeof(cudaGmxSimulation));    
-
-    fprintf( stderr, "In GetCalculateAmoebaCudaWcaDispersionSim: %p %lu %u\n", 
-             gpu->psInteractionCount->_pSysData, gpu->psInteractionCount->_pSysData[0], gpu->sim.workUnits );
-
     RTERROR(status, "GetCalculateAmoebaCudaWcaDispersionSim: cudaMemcpyFromSymbol: SetSim copy from cSim failed");
     status = cudaMemcpyFromSymbol(&amoebaGpu->amoebaSim, cAmoebaSim, sizeof(cudaAmoebaGmxSimulation));    
     RTERROR(status, "GetCalculateAmoebaCudaWcaDispersionSim: cudaMemcpyFromSymbol: SetSim copy from cAmoebaSim failed");
@@ -612,6 +608,7 @@ void kCalculateAmoebaWcaDispersionForces( amoebaGpuContext amoebaGpu )
 
     kReduceWcaDispersionToFloat4( amoebaGpu, gpu->psForce4 );
 
+#ifdef AMOEBA_DEBUG
     if( 0 ){
         gpu->psEnergy->Download();
         double sum = 0.0;
@@ -622,6 +619,7 @@ void kCalculateAmoebaWcaDispersionForces( amoebaGpuContext amoebaGpu )
         }   
         (void) fprintf( amoebaGpu->log,"%14.7e QQ SUM\n", sum );
     }
+#endif
 
     if( 0 ){
         int paddedNumberOfAtoms             = amoebaGpu->gpuContext->sim.paddedNumberOfAtoms;