VM: update_VM.sh fails on GENERATE_SIMULATED_TEST_DATA

[paskino]

Once #743 is fixed, I continued the build but didn't complete.

Got the following error

Scanning dependencies of target MR_PROCESS_TESTDATA
                 from /home/sirfuser/devel/buildVM/sources/SIRF/src/xGadgetron/cGadgetron/tests/mrtest_auxiliary_funs.h:32,
                 from /home/sirfuser/devel/buildVM/sources/SIRF/src/xGadgetron/cGadgetron/tests/mrtests_prep_testdata.cpp:30:
/home/sirfuser/devel/buildVM/sources/SIRF/src/xGadgetron/cGadgetron/include/sirf/Gadgetron/gadgetron_image_wrap.h: In destructor ‘sirf::ImageWrap::~ImageWrap()’
:
                                                                         ^
/home/sirfuser/devel/buildVM/sources/SIRF/src/xGadgetron/cGadgetron/include/sirf/Gadgetron/gadgetron_image_wrap.h:268:4: note: in expansion of macro ‘IMAGE_PROCmpl<boost::exception_detail::error_info_injector<boost::program_options::unknown_option> >'
  what():  unrecognised option '-w'
Child aborted
src/xGadgetron/cGadgetron/tests/CMakeFiles/GENERATE_SIMULATED_TESTDATA.dir/build.make:77: recipe for target 'src/xGadgetron/cGadgetron/tests/CMakeFiles/GENERATE_SIMULATED_TESTDATA' failed

Notice that something crashes.

[paskino]

Is it a Boost error? A version problem? On the VM we are using system Boost

SIRF-SuperBuild/VirtualBox/scripts/UPDATE.sh

Lines 194 to 198 in d9de45b

	-DUSE_SYSTEM_SWIG=On \
	-DUSE_SYSTEM_Boost=On \
	-DUSE_SYSTEM_Armadillo=On \
	-DUSE_SYSTEM_FFTW3=On \
	-DUSE_SYSTEM_HDF5=ON \

[KrisThielemans]

This is a bit confusing. The error is related to boost::program_options::unknown_option which seems to imply it's calling an executable that uses program_options. However, the lines around/above it are SIRF lines. Is this output of a parallel build?

I suspect that the SIRF lines around it are a red-herring and that it's really related to the call to ismrmrd_generate_cartesian_shepp_logan
https://github.com/SyneRBI/SIRF/blob/23a7e7ade525be7f1b84e63f194a0331962699a3/src/xGadgetron/cGadgetron/tests/CMakeLists.txt#L147
which seems to imply it's running on old version of this executable. (Are you upgrading an existing VM?)

[paskino]

Yes, I'm trying to update the VM and got to fix a million lines.

Is it a parallel build? I do not think so as I used update_VM.sh -j1, unless -j1 is treated as a single option, hence discarded!

I think the failing line might be the one you point out.

Shouldn't the update_VM.sh also update the ismrmrd_generate_cartesian_shepp_logan executable?

[KrisThielemans]

I'm trying to update the VM

to be 100% clear. you have an existing VM, and you try to update it. Correct?

got to fix a million lines.

for an existing VM, you will really need the -s option (once)

I used update_VM.sh -j1, unless -j1 is treated as a single option, hence discarded!

I haven't checked bash getopts but I do think you need a space

SIRF-SuperBuild/VirtualBox/scripts/UPDATE.sh

Line 51 in 225b7fa

echo "Usage: $0 [-t tag] [-j n] [-r] [-s]"

Of course, it should have exited with a wrong option

SIRF-SuperBuild/VirtualBox/scripts/UPDATE.sh

Lines 60 to 61 in 225b7fa

	*)
	echo "Wrong option passed. Use the -h option to get some help." >&2

Shouldn't the update_VM.sh also update the ismrmrd_generate_cartesian_shepp_logan executable?

sure, but did it? git status in the sources/ISMRMRD and all that.

[paskino]

I have removed the ISMRMRD build directory before checking, so I can't check that now, but I will do it later on another VM.
Currently I have ISMRMRD v1.7.0 as espected in SIRF-SuperBuild 3.2.0.

The error is as you imagined

Generating Cartesian Shepp Logan Phantom!!!
Acceleration: 1
cd /home/sirfuser/devel/buildVM/builds/SIRF/build/src/xGadgetron/cGadgetron/tests/data/examples/MR && /usr/local/bin/cmake -E env LD_LIBRARY_PATH=/home/sirfuser/devel/install/lib:/home/sirfuser/devel/install/lib:/home/sirfuser/devel/install/lib64:: /home/sirfuser/devel/install/bin/ismrmrd_generate_cartesian_shepp_logan -w 64 -a 2 -o testdata_tmp_2.h5
terminate called after throwing an instance of 'boost::exception_detail::clone_impl<boost::exception_detail::error_info_injector<boost::program_options::unknown_option> >'
  what():  unrecognised option '-w'

[paskino]

now, ismrmrd_generate_cartesian_shepp_logan may be the old one?

sirfuser@vagrant:~/devel/buildVM$ find . | grep ismrmrd_generate_cartesian_shepp_logan

return nothing. It doesn't seem to have been built?

[KrisThielemans]

you could repeat this in ~/devel. Then do an ls -l

it's hard to know what your status is though If you have an existing VM where you messed about a lot. For instance, you wrote

I have removed the ISMRMRD build directory before checking

I'd recommend starting from scratch really.

[paskino]

OK, here's what I did:

rm -rf buildVM
rm -rf install

./SIRF-SuperBuild/VirtualBox/scripts/update_VM.sh -j 4

It ends with a CMake error that ismrmrd_generate_cartesian_shepp_logan cannot be found.

As a matter of fact the executable should be built by ISMRMRD if HDF5, Boost and FFTW3 are found
but they are not

- Could NOT find Boost (missing: random) (found suitable version "1.65.1", minimum required is "1.43")
-- FFTW3 UNIX libraries: /usr/lib/x86_64-linux-gnu/libfftw3.so/usr/lib/x86_64-linux-gnu/libfftw3f.so
-- Found FFTW3: /usr/lib/x86_64-linux-gnu/libfftw3f.so  
FFTW3 or Boost NOT Found, cannot build utilities

But in the 3.1.0 VM Boost random is missing.

[KrisThielemans]

did you use -s? It should install all required boost libraries

[paskino]

Indeed I did not!

[KrisThielemans]

you're going to hit some of the other issues I created then...

[paskino]

Somewhat linked is SyneRBI/SyneRBI_VM#201

[KrisThielemans]

This is now obsolete (after #755 and possibly #758 )