Hi CLAIRE Team,

I hope this message finds you well.

First, thank you for your fantastic work on CLAIRE. I read your manuscript with great interest and I’m genuinely excited to use it in our research with total-body PET. It's not every day someone casually drops a diffeomorphic tool, with heavy parallelization/optimization in mind.

However, I’ve been struggling with the installation process. Despite following the instructions carefully, I’ve run into several issues that I haven’t been able to resolve. This has made it difficult for me to get CLAIRE up and running.

I believe an official Docker image for CLAIRE could make the installation much more straightforward. It would help not only me but also others who might be facing similar challenges. I considered creating a Docker image myself to contribute back, but my difficulties with the initial setup have prevented me from doing so.

Would you consider providing a Docker image for CLAIRE? I think it would be a great help to many in the community. If there’s any way I can assist in this process, please let me know.

Thank you for your time and consideration.

Cheers,
Lalith

@andreasmang:
I am hoping that you can help me with the installation of CLAIRE. Any advice would be very welcome and appreciated. I have performed the following steps. Thanks @tjasaki

1. Installed Nvidia CUDA Toolkit.
   Graphics Card: NVIDIA Corporation TU117GLM [Quadro T2000 Mobile / Max-Q] / Quadro T2000/PCIe/SSE2.
   Processor: Intel® Core™ i9-9880H CPU @ 2.30GHz × 16.
   OS: Ubuntu 20.04.2 LTS.

2. cmake, niftilib, python all operational

3. Installed mpich 3.3.2-2build1 (Ubuntu) (MPI-3.1 standard)

4. mpicc, mpicxx, and nvcc all recognized, with directories
   /usr/bin/mpicc
   /usr/bin/mpicxx
   /usr/bin/nvcc

5. running make from claire-gpu/deps results in the following message:

===============================================================================
Configuring PETSc to compile on your system

=============================================================================== ***** WARNING: MAKEFLAGS (set to ) found in environment variables - ignori use ./configure MAKEFLAGS=$MAKEFLAGS if you really want to use that value=============================================================================== TESTING: check from config.libraries(config/BuildSystem/config/libraries.py:157)*******************************************************************************
UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for details):

Unable to find cuda in default locations!
Perhaps you can specify with --with-cuda-dir=
If you do not want cuda, then give --with-cuda=0

6. Changing makefile with "WITH_CUDA_MPI = no" results in the same message.

7. Changing makefile with "WITH_CUDA_MPI = no" and "BUILD_GPU = no" results in a completed make.

8. Moving forward with this configuration, I set the environment variables using: source env_source.sh

9. I modified the top-level makefile to specify "BUILD_GPU = no" and "WITH_CUDA_MPI = no". Executing :make -j" results in the error mesage

   config.mk:68: *** This branch only supports GPU build. Stop.

10. I reverted back to "BUILD_GPU = yes". Running "make VERBOSE=1 VVERBOSE=1 config" shows the following:

fatal: not a git repository (or any of the parent directories): .git

Options

BUILD_GPU: yes; [yes, no]
BUILD_TEST: no; [yes, no]
BUILD_PYTHON: no; [yes, no]

WITH_NIFTI: yes; [yes, no]
WITH_PNETCDF: no; [yes, no]
WITH_DOUBLE: no; [yes, no]
WITH_DEBUG: no; [yes, no]
WITH_DEVELOP: no; [yes, no]
WITH_CUDA_MPI: no; [yes, no]

BUILD_DIR: ./bin

CXX: mpicxx
NVCC: nvcc

internal build options

BUILD_SHARED: no; [yes, no]
BUILD_TARGET: X86; [POWER9, X86]

MPI_DIR: /usr
CUDA_DIR: /usr
PETSC_DIR: /home/asaki/Software/claire-gpu/deps/lib
NIFTI_DIR: /home/asaki/Software/claire-gpu/deps/lib
ZLIB_DIR: ./
PNETCDF_DIR:
PYTHON_DIR: /usr/include/python3.5

GPU_VERSION:
CPP_VERSION: c++11

APP_DIR: ./apps
SRC_DIR: ./src
OBJ_DIR: ./obj
LIB_DIR: ./lib
EXSRC_DIR: ./3rdparty

CXX_FLAGS:
NVCC_FLAGS:
LD_FLAGS:

I am trying to install Claire on ubuntu 20.04 and am unable to compile.

Error 1:
petscmat.h:685:1: error: ‘PETSC_CXX_INLINE’ does not name a type; did you mean ‘PETSC_C_INLINE’?
685 | PETSC_STATIC_INLINE PetscErrorCode MatGetValue(Mat v,PetscInt i,PetscInt j,PetscScalar *va) {return MatGetValues(v,1,&i,1,&j,va);}

Error 2:
./include/MemoryUtils.hpp: In member function ‘PetscErrorCode reg::ManagedMemory::CopyDeviceToHost()’:
./include/MemoryUtils.hpp:260:3: error: ‘PETSC_FUNCTION_NAME_CXX’ was not declared in this scope; did you mean ‘PETSC_FUNCTION_NAME_C’?
260 | PetscFunctionBegin;

Has anyone else seen these there is a huge barrage of these errors I just selected one instance.

Best,
Ahsan

The link to the libmorton library is broken (at least in the cpu branch).

wget http://users.ices.utexas.edu/~andreas/libs/morton.tar.gz

wget http://math.uh.edu/~andreas/libs/morton.tar.gz

wget https://www.math.uh.edu/~andreas/resources/clairelibs/morton.tar.gz

Issue Description

Hi @andreasmang, what are the contributing guidelines for this project? They are missing from the repository.

Issue Description

Hi @andreasmang, how you have tested/validated your code and it's outputs? Currently, as far as I can find, there is no automated test suite via Github Actions or other.

when using "h1s-stokes" like

./bin/claire -mr ./doc/data/brain01.nii.gz -mt ./doc/data/brain02.nii.gz -regnorm h1s-stokes

return CUDA error string: an illegal memory access was encountered
CUDA error code src/Spectral/mpicufft.cpp:276: 700

other parameters works well

gcc (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
nvcc Build cuda_11.0_bu.TC445_37.28540450_0
petsc 3.14.2
openmpi mpirun (Open MPI) 4.0.3

Dear Claire developers,

Thank you for open sourcing this great package. I would like to ask you, if you have solution to adopt this package to python env. ?
Second question is related to data size, Is this package able of handling data larger than RAM size? Like data with size of terabyte.

I am wondering if Claire has a docker file and if not, are you planning to release one?

original post can be found here: #9 (comment)

the build script for external libraries fails for directories with spaces in the name

I have been unable to install a working copy of claire-gpu. The installation
initially appeared to have completed successfully up until running the makefile:

make -j

The terminal output begins with the message:

fatal: not a git repository (or any of the parent directories): .git

and continues. The next error message is

./include/ReadWriteReg.hpp:29:10: fatal error: pnetcdf.h: No such file or directory
29 | #include "pnetcdf.h"
| ^~~~~~~~~~~
compilation terminated.

Several similar messages appear refering to pnetcdf.h. Working backwards, I
found that that the compilation process ran into a compilation error:

Error during compile, check cxx_opt_sgl/lib/petsc/conf/make.log
Send it and cxx_opt_sgl/lib/petsc/conf/configure.log to [email protected]

The two files in question are included. Note that all dependencies were downloaded/installed using the provided build scipt and all paths have been set.
Thank you for any help you can provide.

Tom

configure.log

make.log

PNETCDF support for multi-GPU code needs to be added (for large-scale applications)