# Dolfinx build issue: Found serial HDF5 build, MPI HDF5 build required **URL:** \ **Category:** General\ **Tags:** dolfinx\ **Created:** [March 12, 2024, 3:02pm UTC](https://fenicsproject.discourse.group/t/dolfinx-build-issue-found-serial-hdf5-build-mpi-hdf5-build-required/13893 "2024-03-12T15:02:17Z")\ **Posts on this page:** 11\ **Page:** 1
**Author:** ![mekong](https://yyz2.discourse-cdn.com/free1/user_avatar/fenicsproject.discourse.group/mekong/32/7729_2.png) [@mekong](https://fenicsproject.discourse.group/u/mekong)\ **Post date:** [March 12, 2024, 3:02pm UTC](https://fenicsproject.discourse.group/t/dolfinx-build-issue-found-serial-hdf5-build-mpi-hdf5-build-required/13893/1 "2024-03-12T15:02:17Z")
Dear all, I am totally new to Fenics and I am having troubles with the installation. I am on OS Sonoma 14.1, and I am trying to install Dolfinx . I followed the build procedure for C++ shown [here](https://docs.fenicsproject.org/dolfinx/main/python/installation.html): `cd dolfinx-main/cpp; mkdir build; cd build; cmake ..` and I get the following output error: ```auto [...] CMake Error at CMakeLists.txt:334 (message): Found serial HDF5 build, MPI HDF5 build required, try setting HDF5_DIR or HDF5_ROOT ``` I installed hdf5 1.14 by downloading the .tar.gz, then ```auto ./configure --enable-parallel --enable-shared make sudo make install ``` If I remove `--enable-parallel` , `--enable-shared` or both, I get the same error. Do you know how to fix this ? Thank you ! ---
**Author:** ![francesco-ballarin](https://avatars.discourse-cdn.com/v4/letter/f/f05b48/32.png) [@francesco-ballarin](https://fenicsproject.discourse.group/u/francesco-ballarin)\ **Post date:** [March 12, 2024, 3:17pm UTC](https://fenicsproject.discourse.group/t/dolfinx-build-issue-found-serial-hdf5-build-mpi-hdf5-build-required/13893/2 "2024-03-12T15:17:52Z")
You may want to > [@mekong](#): > > ```auto > try setting HDF5_DIR or HDF5_ROOT > > ``` to the directory where > [@mekong](#): > > ```auto > sudo make install > > ``` installed your custom version of hdf5. To be extra safe, delete the `build` folder before running `cmake` again. ---
**Author:** ![mekong](https://yyz2.discourse-cdn.com/free1/user_avatar/fenicsproject.discourse.group/mekong/32/7729_2.png) [@mekong](https://fenicsproject.discourse.group/u/mekong)\ **Post date:** [March 12, 2024, 3:36pm UTC](https://fenicsproject.discourse.group/t/dolfinx-build-issue-found-serial-hdf5-build-mpi-hdf5-build-required/13893/3 "2024-03-12T15:36:02Z")
> [@mekong](#): > > `setting HDF5_DIR` Hello, I don’t understand, where should I set `HDF5_DIR` ? In .bash\_profile or .zprofile ? ---
**Author:** ![francesco-ballarin](https://avatars.discourse-cdn.com/v4/letter/f/f05b48/32.png) [@francesco-ballarin](https://fenicsproject.discourse.group/u/francesco-ballarin)\ **Post date:** [March 12, 2024, 3:46pm UTC](https://fenicsproject.discourse.group/t/dolfinx-build-issue-found-serial-hdf5-build-mpi-hdf5-build-required/13893/4 "2024-03-12T15:46:54Z")
Try with `export HDF5_ROOT=/path/to/hdf5` in your current terminal, no need to modify profile files, delete `build` and run `cmake` again. You may use tools like `ccmake` in your build directory to double check whether this setting makes any difference. ---
**Author:** ![mekong](https://yyz2.discourse-cdn.com/free1/user_avatar/fenicsproject.discourse.group/mekong/32/7729_2.png) [@mekong](https://fenicsproject.discourse.group/u/mekong)\ **Post date:** [March 12, 2024, 3:57pm UTC](https://fenicsproject.discourse.group/t/dolfinx-build-issue-found-serial-hdf5-build-mpi-hdf5-build-required/13893/5 "2024-03-12T15:57:33Z")
> [@francesco-ballarin](#): > > export HDF5\_ROOT=/path/to/hdf5 Hello, I am not sure what is the right folder to set to `/path/to/hdf5`. It may be `/Applications/hdf5-1.14.3/hdf5/` or `/Applications/hdf5-1.14.3/hdf5/bin/`? Here is what is inside these folders: ` % ls /Applications/hdf5-1.14.3/hdf5/bin h5cc h5debug h5dump h5import h5mkgrp h5perf_serial h5repart h5unjam h5clear h5delete h5format_convert h5jam h5pcc h5redeploy h5stat h5watch h5copy h5diff h5fuse.sh h5ls h5perf h5repack h5tools_test_utils ph5diff` ` % ls /Applications/hdf5-1.14.3/hdf5/ bin include lib share` Anyway, I removed the `build` folder, then did `export HDF5_ROOT=/Applications/hdf5-1.14.3/hdf5/bin; mkdir build; cd build; cmake .. ` but I still get the same error message. I also get the same error message if I replace `/Applications/hdf5-1.14.3/hdf5/bin` with `/Applications/hdf5-1.14.3/hdf5/` ---
**Author:** ![francesco-ballarin](https://avatars.discourse-cdn.com/v4/letter/f/f05b48/32.png) [@francesco-ballarin](https://fenicsproject.discourse.group/u/francesco-ballarin)\ **Post date:** [March 12, 2024, 5:44pm UTC](https://fenicsproject.discourse.group/t/dolfinx-build-issue-found-serial-hdf5-build-mpi-hdf5-build-required/13893/6 "2024-03-12T17:44:04Z")
It’s definitely the one without bin. Double check with ccmake that it the one actually being used while building dolfinx. ---
**Author:** ![mekong](https://yyz2.discourse-cdn.com/free1/user_avatar/fenicsproject.discourse.group/mekong/32/7729_2.png) [@mekong](https://fenicsproject.discourse.group/u/mekong)\ **Post date:** [March 12, 2024, 9:49pm UTC](https://fenicsproject.discourse.group/t/dolfinx-build-issue-found-serial-hdf5-build-mpi-hdf5-build-required/13893/7 "2024-03-12T21:49:21Z")
Hello, I used the one without bin, here is the output given by ccmake : ```auto $ccmake .. Page 1 of 1 BUILD_SHARED_LIBS ON Basix_DIR /usr/local/lib/cmake/basix Boost_INCLUDE_DIR /opt/homebrew/include Boost_TIMER_LIBRARY_RELEASE /opt/homebrew/lib/libboost_timer-mt.dylib CMAKE_BUILD_TYPE RelWithDebInfo CMAKE_INSTALL_PREFIX /usr/local CMAKE_INSTALL_RPATH_USE_LINK_P ON CMAKE_OSX_ARCHITECTURES CMAKE_OSX_DEPLOYMENT_TARGET 14.1 CMAKE_OSX_SYSROOT /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.2.sdk DOLFINX_ENABLE_ADIOS2 ON DOLFINX_ENABLE_KAHIP OFF DOLFINX_ENABLE_PARMETIS ON DOLFINX_ENABLE_SCOTCH ON DOLFINX_ENABLE_SLEPC ON DOLFINX_SKIP_BUILD_TESTS OFF DOLFINX_UFCX_PYTHON ON DOXYGEN_DOLFINX_VERSION 0.8.0.0 GIT_FOUND /opt/homebrew/bin/git HDF5_C_LIBRARY_dl /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.2.sdk/usr/lib/libdl.tbd HDF5_C_LIBRARY_hdf5 /Applications/hdf5-1.14.3/hdf5/lib/libhdf5.dylib HDF5_C_LIBRARY_m /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.2.sdk/usr/lib/libm.tbd HDF5_C_LIBRARY_z /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.2.sdk/usr/lib/libz.tbd _REQUIRE_ADIOS2 OFF _REQUIRE_KAHIP OFF _REQUIRE_PARMETIS OFF _REQUIRE_SCOTCH OFF _REQUIRE_SLEPC OFF _UFCX_HEADER _UFCX_HEADER-NOTFOUND pugixml_DIR /opt/homebrew/lib/cmake/pugixml ``` I don’t see any `HDF5_ROOT` though, I don’t understand … ---
**Author:** ![francesco-ballarin](https://avatars.discourse-cdn.com/v4/letter/f/f05b48/32.png) [@francesco-ballarin](https://fenicsproject.discourse.group/u/francesco-ballarin)\ **Post date:** [March 13, 2024, 9:32am UTC](https://fenicsproject.discourse.group/t/dolfinx-build-issue-found-serial-hdf5-build-mpi-hdf5-build-required/13893/8 "2024-03-13T09:32:22Z")
This is the relevant line > [@mekong](#): > > `HDF5_C_LIBRARY_hdf5 /Applications/hdf5-1.14.3/hdf5/lib/libhdf5.dylib` which seems to confirm that hdf5 was taken from the path you provided. However, are you sure that it is actually the path were you installed your custom hdf5 version? I am no mac user, but it seems odd that > [@mekong](#): > > ```auto > Basix_DIR /usr/local/lib/cmake/basix > CMAKE_INSTALL_PREFIX /usr/local > > ``` basix and dolfinx would get installed in `/usr/local` when you build them manually, which would make me think that also your custom hdf5 installation was installed in `/usr/local` ---
**Author:** ![mekong](https://yyz2.discourse-cdn.com/free1/user_avatar/fenicsproject.discourse.group/mekong/32/7729_2.png) [@mekong](https://fenicsproject.discourse.group/u/mekong)\ **Post date:** [March 13, 2024, 10:35am UTC](https://fenicsproject.discourse.group/t/dolfinx-build-issue-found-serial-hdf5-build-mpi-hdf5-build-required/13893/9 "2024-03-13T10:35:07Z")
Hello, The output of ` sudo make install` in the hdf5 installation directory is ```auto [...] + /usr/bin/install -c ./ex_table_12.c /Applications/hdf5-1.14.3/hdf5/share/hdf5_examples/hl/c/. + /usr/bin/install -c ./ex_ds1.c /Applications/hdf5-1.14.3/hdf5/share/hdf5_examples/hl/c/. + /usr/bin/install -c ./image24pixel.txt /Applications/hdf5-1.14.3/hdf5/share/hdf5_examples/hl/c/. [...] ``` so I guess that my custom installation of hdf5 was installed in /Applications/hdf5-1.14.3/hdf5/. Now if I do `export HDF5_ROOT=/Applications/hdf5-1.14.3/hdf5/` and - install hdft with ` ./configure; make; make install`, - run `cmake ..` in `/Applications/dolfinx-main/cpp/build` - I get the error message of the original post. However, if I - install hdf5 with ` ./configure --enable-parallel --enable-shared; make; make install` - run `cmake ..` in `/Applications/dolfinx-main/cpp/build` - I get another error message `Could NOT find UFCx (missing: UFCX_INCLUDE_DIRS UFCX_SIGNATURE UFCX_VERSION) (Required is at least version "0.7")`. Let alone the new error message, this means that adding the flags to configure fixed the issue with hdf5? Thanks ---
**Author:** ![francesco-ballarin](https://avatars.discourse-cdn.com/v4/letter/f/f05b48/32.png) [@francesco-ballarin](https://fenicsproject.discourse.group/u/francesco-ballarin)\ **Post date:** [March 13, 2024, 2:07pm UTC](https://fenicsproject.discourse.group/t/dolfinx-build-issue-found-serial-hdf5-build-mpi-hdf5-build-required/13893/10 "2024-03-13T14:07:22Z")
It means that now hdf5 is ok, the ufcx error is unrelated, and I will look into that in the other post you opened. ---
**Author:** ![mekong](https://yyz2.discourse-cdn.com/free1/user_avatar/fenicsproject.discourse.group/mekong/32/7729_2.png) [@mekong](https://fenicsproject.discourse.group/u/mekong)\ **Post date:** [March 13, 2024, 4:43pm UTC](https://fenicsproject.discourse.group/t/dolfinx-build-issue-found-serial-hdf5-build-mpi-hdf5-build-required/13893/11 "2024-03-13T16:43:12Z")
Great, Thank you! Best,