Compilation on Linux - Githubissues

Some (unofficial) tips for those who want to use WarpLib from Linux.

Use Mono 5.18 and csc, not msc.

liblion

Get it from https://github.com/dtegunov/liblion. Apply several changes I reported there:

gtom

Get it from https://github.com/dtegunov/gtom and compile to make libgtom.a.

As reported in https://github.com/dtegunov/gtom/issues, some tests do not compile; just comment them out.

Windows specific function signatures

They should be disabled.

GPUAcceleration/Functions.h:

#define dllexport
#define __declspec(x)
#define __stdcall

Aligned malloc is not present in Linux

Use fftw_malloc instead in GPUAcceleration/einspline/blip_create.c.

Tensorflow C API

Use pre-compiled binary from Google https://www.tensorflow.org/install/lang_c.

--- a/WarpLib/Tools/TFHelper.cs
+++ b/WarpLib/Tools/TFHelper.cs
@@ -68,7 +68,8 @@ namespace Warp.Tools

         // extern TF_Session * TF_LoadSessionFromSavedModel (const TF_SessionOptions *session_options, const TF_Buffer 
         [DllImport(NativeBinding.TensorFlowLibrary)]
-        static extern unsafe TF_Session TF_LoadSessionFromSavedModelOnDevice(TF_SessionOptions session_options, LLBuffer* run_options, string export_dir, string[] tags, int tags_len, TF_Graph graph, string device, TF_Status status);
+        static extern unsafe TF_Session TF_LoadSessionFromSavedModel(TF_SessionOptions session_options, LLBuffer* run_options, string export_dir, string[] tags, int tags_len, TF_Graph graph, LLBuffer* meta_graph_def, TF_Status status);

@@ -94,9 +95,10 @@ namespace Warp.Tools
             var cstatus = TFStatus.Setup(status);
             unsafe
             {
-                var h = TF_LoadSessionFromSavedModelOnDevice(sessionOptions.handle, runOptions == null ? null : runOptions.LLBuffer, exportDir, tags, tags.Length, graph.handle, device, cstatus.handle);
+                var h = TF_LoadSessionFromSavedModel(sessionOptions.handle, runOptions == null ? null : runOptions.LLBuffer, exportDir, tags, tags.Length, graph.handle, null, cstatus.handle);

GPUAccleration.dll

PROGRAM = GPUAcceleration.dll
NVCC = nvcc
NVCCFLAGS = --compiler-options "-fPIC -std=c++11 -mavx -march=native" -I/path/to/liblion -I../GPUAcceleration/include -I../GPUAcceleration/einspline 

OBJS = ../GPUAcceleration/Angles.o ../GPUAcceleration/Comparison.o ../GPUAcceleration/Device.o ../GPUAcceleration/ParticleCTF.o \
       ../GPUAcceleration/Polishing.o ../GPUAcceleration/SparseEigen.o ../GPUAcceleration/Backprojection.o \
       ../GPUAcceleration/Correlation.o ../GPUAcceleration/Einspline.o ../GPUAcceleration/ParticleMultiBody.o \
       ../GPUAcceleration/Post.o ../GPUAcceleration/Symmetry.o ../GPUAcceleration/Bessel.o ../GPUAcceleration/Cubic.o \
       ../GPUAcceleration/FFT.o ../GPUAcceleration/ParticleNMA.o ../GPUAcceleration/Projector.o ../GPUAcceleration/TomoRefine.o \
       ../GPUAcceleration/BoxNet2.o ../GPUAcceleration/CubicGPU.o ../GPUAcceleration/FSC.o ../GPUAcceleration/ParticleShift.o \
       ../GPUAcceleration/Raycast.o ../GPUAcceleration/Tools.o ../GPUAcceleration/CTF.o ../GPUAcceleration/Deconv.o ../GPUAcceleration/Memory.o \
       ../GPUAcceleration/ParticleSoftBody.o ../GPUAcceleration/Shift.o ../GPUAcceleration/WeightOptimization.o \
       ../GPUAcceleration/einspline/bspline_create.o \
       ../../liblion/src/filename.o ../../liblion/src/backprojector.o ../../liblion/src/complex.o ../../liblion/src/ctf.o \
       ../../liblion/src/euler.o ../../liblion/src/healpix_sampling.o ../../liblion/src/multidim_array.o \
       ../../liblion/src/mask.o ../../liblion/src/projector.o ../../liblion/src/symmetries.o ../../liblion/src/funcs.o \
       ../../liblion/src/numerical_recipes.o ../../liblion/src/fftw.o

%.o: %.cpp
        $(NVCC) $(NVCCFLAGS) -c -o $@ $<

%.o: %.cu
        $(NVCC) $(NVCCFLAGS) -c -o $@ $<

$(PROGRAM): $(OBJS)
        $(NVCC) $(NVCCFLAGS) --shared -o $(PROGRAM) ../../gtom/build/lib/libgtom.a /path/to/relion/external/fftw/lib/libfftw3f.a $^

.PHONY: clean
clean:
        rm -fr $(PROGRAM) $(OBJS)

This quick and dirty Makefile does not recompile the binary when the header file is modified.

WarpLib.dll

~/local/mono-5.14/bin/csc -debug /t:library /out:WarpLib.dll /unsafe \
 /reference:System.Drawing.dll /reference:Accord.dll /reference:Accord.Math.dll /reference:Accord.Math.Core.dll /reference:MathNet.Numerics.dll \
 /reference:BitMiracle.LibTiff.NET.dll /reference:System.Numerics.dll \
../WarpLib/GPUQueue.cs ../WarpLib/NMAMap.cs ../WarpLib/Tools/ByteReaderBE.cs ../WarpLib/Tools/Matrix3.cs \
../WarpLib/Headers/DM4.cs ../WarpLib/Tools/ClusterTrieste.cs ../WarpLib/Tools/Matrix4.cs \
../WarpLib/CPU.cs ../WarpLib/Headers/EM.cs ../WarpLib/Tools/FloatVectors.cs ../WarpLib/Tools/PhysicsHelper.cs \
../WarpLib/CTF.cs ../WarpLib/Headers/Headers.cs ../WarpLib/ProcessingOptions.cs ../WarpLib/Tools/Helper.cs ../WarpLib/Tools/Quaternion.cs \
../WarpLib/Cubic1D.cs ../WarpLib/Headers/MRC.cs ../WarpLib/Projector.cs ../WarpLib/Tools/ImageHelper.cs ../WarpLib/Tools/RandomNormal.cs \
../WarpLib/Cubic1DShort.cs ../WarpLib/Headers/Raw.cs ../WarpLib/SoftMap.cs ../WarpLib/Tools/IntVectors.cs ../WarpLib/Tools/Symmetry.cs \
../WarpLib/CubicGrid.cs ../WarpLib/Star.cs ../WarpLib/Tools/IOHelper.cs \
../WarpLib/FSC.cs ../WarpLib/Image.cs ../WarpLib/Tools/Logger.cs ../WarpLib/Tools/XMLHelper.cs \
../WarpLib/GPU.cs ../WarpLib/Movie.cs ../WarpLib/Tools/BenchmarkTimer.cs ../WarpLib/Tools/MathHelper.cs ../WarpLib/WarpBase.cs \
../WarpLib/TensorFlowSharp/Buffer.cs ../WarpLib/TensorFlowSharp/Operations.g.cs ../WarpLib/TensorFlowSharp/Tensor.cs ../WarpLib/TensorFlowSharp/Variable.cs \
../WarpLib/TensorFlowSharp/OperationsExtras.cs ../WarpLib/TensorFlowSharp/Queue.cs ../WarpLib/TensorFlowSharp/Tensorflow.cs \
../WarpLib/NoiseNet3D.cs ../WarpLib/BoxNet2.cs ../WarpLib/BoxNet.cs ../WarpLib/Tools/TFHelper.cs ../WarpLib/Headers/Tiff.cs \
../WarpLib/NoiseNet2D.cs

Binary

You need your own main.cs. Interesting functions to call are Movie.ProcessCTF and Movie.ProcessShift.

 ~/local/mono-5.14/bin/csc /unsafe /out:WarpConsole.exe /reference:WarpLib.dll /reference:CommandLine.dll main.cs

cramerlab / warp

Compilation on Linux #5