# Problem with linked packages in the getall file **URL:** \ **Category:** FreeFEM installation\ **Created:** [March 14, 2024, 1:18pm UTC](https://community.freefem.org/t/problem-with-linked-packages-in-the-getall-file/3037 "2024-03-14T13:18:20Z")\ **Posts on this page:** 14\ **Page:** 1
**Author:** ![Andres](https://avatars.discourse-cdn.com/v4/letter/a/a4c791/32.png) [@Andres](https://community.freefem.org/u/Andres)\ **Post date:** [March 14, 2024, 1:18pm UTC](https://community.freefem.org/t/problem-with-linked-packages-in-the-getall-file/3037/1 "2024-03-14T13:18:20Z")
I am trying to make the installation in Ubuntu 20.04, I did this many time on 18.04, but now when I run the command **./3rdparty/getall -a** there are many packages that cannot be accessed or downloaded. I checked the getall file trying to access myself from Chrome to some of those links such as : **download(‘ARPACK’,‘[http://www.caam.rice.edu/software/ARPACK/SRC/arpack96.tar.gz](http://www.caam.rice.edu/software/ARPACK/SRC/arpack96.tar.gz)’,** \*\* ‘[http://www.caam.rice.edu/software/ARPACK](http://www.caam.rice.edu/software/ARPACK)’,\*\* \*\* ‘arpack96.tar.gz’,\*\* \*\* ‘fffaa970198b285676f4156cebc8626e’);\*\* but that page does not exist, it is an error. Then, this problem also affects the subsequent installation steps. ---
**Author:** ![frederichecht](https://yyz2.discourse-cdn.com/flex030/user_avatar/community.freefem.org/frederichecht/32/15_2.png) [@frederichecht](https://community.freefem.org/u/frederichecht)\ **Post date:** [March 14, 2024, 3:27pm UTC](https://community.freefem.org/t/problem-with-linked-packages-in-the-getall-file/3037/2 "2024-03-14T15:27:17Z")
I will check the getall script Thank, ---
**Author:** ![prj](https://avatars.discourse-cdn.com/v4/letter/p/ecae2f/32.png) [@prj](https://community.freefem.org/u/prj)\ **Post date:** [March 14, 2024, 3:29pm UTC](https://community.freefem.org/t/problem-with-linked-packages-in-the-getall-file/3037/3 "2024-03-14T15:29:01Z")
You can let PETSc install ARPACK (via `make petsc-slepc`), then, you won’t have issues with getall. Most of the links in getall are out-dated, so you should not rely on them anyway. ---
**Author:** ![Andres](https://avatars.discourse-cdn.com/v4/letter/a/a4c791/32.png) [@Andres](https://community.freefem.org/u/Andres)\ **Post date:** [March 14, 2024, 3:47pm UTC](https://community.freefem.org/t/problem-with-linked-packages-in-the-getall-file/3037/4 "2024-03-14T15:47:15Z")
It means that I don’t need to use “./3rdparty/getall -a” and then I can skip from step 4 to 6 in the installation instructions? Many thanks ---
**Author:** ![prj](https://avatars.discourse-cdn.com/v4/letter/p/ecae2f/32.png) [@prj](https://community.freefem.org/u/prj)\ **Post date:** [March 14, 2024, 3:57pm UTC](https://community.freefem.org/t/problem-with-linked-packages-in-the-getall-file/3037/5 "2024-03-14T15:57:54Z")
I don’t know what installation instructions you are using, almost all of them are also out-dated. If you follow these steps [GitHub - FreeFem/FreeFem-sources: FreeFEM source code](https://github.com/FreeFem/FreeFem-sources?tab=readme-ov-file#freefem), you should be good to go. ---
**Author:** ![Andres](https://avatars.discourse-cdn.com/v4/letter/a/a4c791/32.png) [@Andres](https://community.freefem.org/u/Andres)\ **Post date:** [March 14, 2024, 4:14pm UTC](https://community.freefem.org/t/problem-with-linked-packages-in-the-getall-file/3037/6 "2024-03-14T16:14:03Z")
I was following this [https://doc.freefem.org/introduction/installation.html](https://Ubuntu-Instructions), the only difference is the prefix. Then, following the instructions you suggested, as “./3rdparty/getall -a” is not working well because of the getall file is out-dated, I forced all the installations using “make petsc-slepc” directly. At the end the problem of the links persists when I excecute make -j2, many errors appear. ---
**Author:** ![prj](https://avatars.discourse-cdn.com/v4/letter/p/ecae2f/32.png) [@prj](https://community.freefem.org/u/prj)\ **Post date:** [March 14, 2024, 4:28pm UTC](https://community.freefem.org/t/problem-with-linked-packages-in-the-getall-file/3037/7 "2024-03-14T16:28:35Z")
What do you mean? What errors? ---
**Author:** ![Andres](https://avatars.discourse-cdn.com/v4/letter/a/a4c791/32.png) [@Andres](https://community.freefem.org/u/Andres)\ **Post date:** [March 14, 2024, 8:09pm UTC](https://community.freefem.org/t/problem-with-linked-packages-in-the-getall-file/3037/8 "2024-03-14T20:09:55Z")
The problem was finally solve apdating in getall the mmg and parmmg packages: ![Selection_022](https://canada1.discourse-cdn.com/flex030/uploads/freefem/original/2X/e/e4320b07ba1971ea45a28d537ad3c84a4226c2a3.png) After doing sudo make -j4, the example testvtk.edp in /examples/3dSurf/ did not working, looking at its .log file I commented the last three lines: //savevtk(“ThL.vtk”,ThL,bin=1); //savevtk(“ThL.vtu”,ThL,bin=1); //meshL ThL2=vtkloadL(“ThL.vtk”); This problem was previously reported [here](https://community.freefem.org/t/make-check-on-ubuntu-23-10-fails-testvtk-edp/2851/9) Then I could run sudo make -j4 and sudo make -j4 check, with the following results: XFAIL: stokes-adapt-3d-PETSc.edp SKIP: PARDISO.edp However, for my purpose parallel freefem is working well now! Cheers, ---
**Author:** ![fagnelli](https://yyz2.discourse-cdn.com/flex030/user_avatar/community.freefem.org/fagnelli/32/1211_2.png) [@fagnelli](https://community.freefem.org/u/fagnelli)\ **Post date:** [March 29, 2024, 11:56pm UTC](https://community.freefem.org/t/problem-with-linked-packages-in-the-getall-file/3037/9 "2024-03-29T23:56:28Z")
Hi everyone, I am having difficulties to install the last version of FreeFem from sources recently on Ubuntu 22.04. The errors message that I received seem related to the conversation above. First: I have following the installation instructions specified in @prj 's message (the instructions link are here: [GitHub - FreeFem/FreeFem-sources: FreeFEM source code](https://github.com/FreeFem/FreeFem-sources?tab=readme-ov-file#freefem)) I received an error while executing: `./3rdparty/getall -a` Second, I changed this line with: `./3rdparty/getall -o PETSc -a` I am now stuck with many errors during the final make process. Below is the error message: ```auto 34.73 ERROR: ../bin/build/download http://104.46.50.187/pkg/freeyams.2012.02.05.tgz pkg/freeyams.2012.02.05.tgz FAILED 34.73 ERROR 2: ../bin/build/download http://pkgs.freefem.org/freeyams.2012.02.05.tgz pkg/freeyams.2012.02.05.tgz FAILED 34.73 ERROR2: INVALID MD5 for freeyams.2012.02.05.tgz d41d8cd98f00b204e9800998ecf8427e 34.73 make[5]: Leaving directory '/usr/local/src/FreeFem-sources/3rdparty/yams' 34.73 make[5]: *** [Makefile:71: ../pkg/freeyams.2012.02.05.tgz] Error 1 34.73 make[4]: *** [Makefile:1015: compile-dir] Error 2 34.73 make[4]: Leaving directory '/usr/local/src/FreeFem-sources/3rdparty' 34.73 make[3]: *** [Makefile:1024: tag-compile-pkg] Error 1 34.73 make[3]: Leaving directory '/usr/local/src/FreeFem-sources/3rdparty' 34.73 make[2]: *** [Makefile:615: all-recursive] Error 1 34.73 make[2]: Leaving directory '/usr/local/src/FreeFem-sources/3rdparty' 34.73 make[1]: *** [Makefile:808: all-recursive] Error 1 34.73 make[1]: Leaving directory '/usr/local/src/FreeFem-sources' 34.73 make: *** [Makefile:758: all] Error 2 ``` I have tested some modifications, but now I am running out of ideas to move forward with the installation. Do you deem the problem is only related to the getall file? ---
**Author:** ![prj](https://avatars.discourse-cdn.com/v4/letter/p/ecae2f/32.png) [@prj](https://community.freefem.org/u/prj)\ **Post date:** [March 30, 2024, 6:10am UTC](https://community.freefem.org/t/problem-with-linked-packages-in-the-getall-file/3037/10 "2024-03-30T06:10:36Z")
Could you simply go into the `src` subfolder and type `make `? ---
**Author:** ![fagnelli](https://yyz2.discourse-cdn.com/flex030/user_avatar/community.freefem.org/fagnelli/32/1211_2.png) [@fagnelli](https://community.freefem.org/u/fagnelli)\ **Post date:** [April 1, 2024, 4:08pm UTC](https://community.freefem.org/t/problem-with-linked-packages-in-the-getall-file/3037/11 "2024-04-01T16:08:11Z")
Ok, I have tried to rebuild FreeFem from sources, by doing: ```auto autoreconf -i ./configure --enable-download --enable-optim --prefix=/usr/local/freefem/ ./3rdparty/getall -o PETSc -a cd 3rdparty/ff-petsc make petsc-slepc cd - ./reconfigure ``` Finally I have done: `cd src && make` Upon running make, I get this error: ```auto make[1]: Entering directory '/usr/local/src/FreeFem-sources/src/mpi' cp ../fflib/ffapi.cpp . depbase=`echo ffapi.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ /usr/bin/mpic++ -DHAVE_CONFIG_H -I. -I../.. -DPARALLELE -I./../fflib -I./../Graphics -I./../femlib -I./../bamglib/ -I/usr/include/x86_64-linux-gnu/mpich -I/usr/include -I/usr/include/hdf5/serial -I/usr/local/freefem/ff-petsc/r/include -I/usr/local/freefem/ff-petsc/c/include -DWITH_bemtool -DWITH_htool -I./../../3rdparty/include/BemTool/ -I./../../3rdparty/boost/include -I../../plugin/mpi -DPARALLELE -DHAVE_ZLIB -g -O2 -DNDEBUG -O3 -mtune=generic -std=gnu++14 -DBAMG_LONG_LONG -DNCHECKPTR -fPIC -MT ffapi.o -MD -MP -MF $depbase.Tpo -c -o ffapi.o ffapi.cpp &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo ../lglib/mymain.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ /usr/bin/mpic++ -DHAVE_CONFIG_H -I. -I../.. -DPARALLELE -I./../fflib -I./../Graphics -I./../femlib -I./../bamglib/ -I/usr/include/x86_64-linux-gnu/mpich -I/usr/include -I/usr/include/hdf5/serial -I/usr/local/freefem/ff-petsc/r/include -I/usr/local/freefem/ff-petsc/c/include -DWITH_bemtool -DWITH_htool -I./../../3rdparty/include/BemTool/ -I./../../3rdparty/boost/include -I../../plugin/mpi -DPARALLELE -DHAVE_ZLIB -g -O2 -DNDEBUG -O3 -mtune=generic -std=gnu++14 -DBAMG_LONG_LONG -DNCHECKPTR -fPIC -MT ../lglib/mymain.o -MD -MP -MF $depbase.Tpo -c -o ../lglib/mymain.o ../lglib/mymain.cpp &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo ../lglib/lg.tab.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ /usr/bin/mpic++ -DHAVE_CONFIG_H -I. -I../.. -DPARALLELE -I./../fflib -I./../Graphics -I./../femlib -I./../bamglib/ -I/usr/include/x86_64-linux-gnu/mpich -I/usr/include -I/usr/include/hdf5/serial -I/usr/local/freefem/ff-petsc/r/include -I/usr/local/freefem/ff-petsc/c/include -DWITH_bemtool -DWITH_htool -I./../../3rdparty/include/BemTool/ -I./../../3rdparty/boost/include -I../../plugin/mpi -DPARALLELE -DHAVE_ZLIB -g -O2 -DNDEBUG -O3 -mtune=generic -std=gnu++14 -DBAMG_LONG_LONG -DNCHECKPTR -fPIC -MT ../lglib/lg.tab.o -MD -MP -MF $depbase.Tpo -c -o ../lglib/lg.tab.o ../lglib/lg.tab.cpp &&\ mv -f $depbase.Tpo $depbase.Po cp ../fflib/compositeFESpace.cpp . depbase=`echo compositeFESpace.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ /usr/bin/mpic++ -DHAVE_CONFIG_H -I. -I../.. -DPARALLELE -I./../fflib -I./../Graphics -I./../femlib -I./../bamglib/ -I/usr/include/x86_64-linux-gnu/mpich -I/usr/include -I/usr/include/hdf5/serial -I/usr/local/freefem/ff-petsc/r/include -I/usr/local/freefem/ff-petsc/c/include -DWITH_bemtool -DWITH_htool -I./../../3rdparty/include/BemTool/ -I./../../3rdparty/boost/include -I../../plugin/mpi -DPARALLELE -DHAVE_ZLIB -g -O2 -DNDEBUG -O3 -mtune=generic -std=gnu++14 -DBAMG_LONG_LONG -DNCHECKPTR -fPIC -MT compositeFESpace.o -MD -MP -MF $depbase.Tpo -c -o compositeFESpace.o compositeFESpace.cpp &&\ mv -f $depbase.Tpo $depbase.Po compositeFESpace.cpp:17:10: fatal error: bemtool/tools.hpp: No such file or directory 17 | #include | ^ ~~~~~~~~~~~~~~~~~~ compilation terminated. make[1]: *** [Makefile:708: compositeFESpace.o] Error 1 make[1]: Leaving directory '/usr/local/src/FreeFem-sources/src/mpi' make: *** [Makefile:552: all-recursive] Error 1 ``` ---
**Author:** ![clthu](https://avatars.discourse-cdn.com/v4/letter/c/f04885/32.png) [@clthu](https://community.freefem.org/u/clthu)\ **Post date:** [April 23, 2024, 4:04am UTC](https://community.freefem.org/t/problem-with-linked-packages-in-the-getall-file/3037/12 "2024-04-23T04:04:41Z")
I met the same problem like this when I updated my FreeFEM++ from version 4.12 to 4.14. I thought this might be related to some packages in the 3rdparty/pkg were not downloaded successfully ---
**Author:** ![clthu](https://avatars.discourse-cdn.com/v4/letter/c/f04885/32.png) [@clthu](https://community.freefem.org/u/clthu)\ **Post date:** [April 23, 2024, 4:17am UTC](https://community.freefem.org/t/problem-with-linked-packages-in-the-getall-file/3037/13 "2024-04-23T04:17:10Z")
I finally succeeded when I try “cd src && make” . (But I thought it might be helpful to download the needed package manually and put them in the folder 3rdparty/pkg… it’s strange that PETSc could not install these packages automatically in some cases, even one year ago I didn’t meet any problem to install version 4.12 ) ---
**Author:** ![prj](https://avatars.discourse-cdn.com/v4/letter/p/ecae2f/32.png) [@prj](https://community.freefem.org/u/prj)\ **Post date:** [April 23, 2024, 5:27am UTC](https://community.freefem.org/t/problem-with-linked-packages-in-the-getall-file/3037/14 "2024-04-23T05:27:00Z")
BemTool is not part of PETSc, most of the other packages are indeed installed by PETSc.