Thank you. I guess since I am on a virtual machine when I say
./configure --enable-download --without-hd5 --prefix=${PWD}
I get the error
–prefix=/home/ceren/Desktop/FreeFem resources: no such file or directory. I am not sure how to define prefix to a vm folder. Any experience on that?
You are not typing the proper command on your machine, probably missing space, or extra new line, or something.
I copy pasted from the document shared, but will check again. ${pwd} looks for a folder in my windows machine I guess (and not on ubuntu vm where I am trying to do the installation on) and that might be the source of the problem.
Do not copy/paste, type in full. Depending on your PDF viewer, some characters may not be copy/paste’d correctly, e.g., -- becomes –.
you are right, that was actually the problem.
Hello again,
I did follow the instructions on pdf and tried to compile the developer version (I am not sure if I sucsessfully did). However, I can not launch the example scripts using binaries of FreeFem (none works). I tried attaching config.log file that might point out the problem during installation which I do not understand, but I could not.
Thank you,
What error do you get? “None works” is not a very informative message…
What do you mean they did not work ? Any errors?
First try “which FreeFem++” and make sure that points to the right one.
I’m not entirely sure what you are doing but in the absence of a specific
better idea, try running ldd on the
binaries and post here Probably there are issues with the LD_LIBRARY_PATH
among others. For example, look at output like this for any thing that is
not resolved or points to something stale/wrong.
ldd `which FreeFem++`
linux-vdso.so.1 (0x00007ffd42384000)
libumfpack.so.5 => /home/ubuntu/dev/freefem/install/ff-petsc/r/lib/libumfpack.so.5 (0x00007fd55cbbe000)
libcholmod.so.3 => /home/ubuntu/dev/freefem/install/ff-petsc/r/lib/libcholmod.so.3 (0x00007fd55cab5000)
libarpack.so.2 => /home/ubuntu/dev/freefem/install/ff-petsc/r/lib/libarpack.so.2 (0x00007fd55ca68000)
libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007fd55ca37000)
libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007fd55c8e8000)
libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6 (0x00007fd55c704000)
libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007fd55c6e9000)
libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007fd55c4f7000)
libamd.so.2 => /home/ubuntu/dev/freefem/install/ff-petsc/r/lib/libamd.so.2 (0x00007fd55c4eb000)
libsuitesparseconfig.so.5 => /home/ubuntu/dev/freefem/install/ff-petsc/r/lib/libsuitesparseconfig.so.5 (0x00007fd55c4e6000)
libblas.so.3 => /usr/lib/x86_64-linux-gnu/libblas.so.3 (0x00007fd55c477000)
libcolamd.so.2 => /home/ubuntu/dev/freefem/install/ff-petsc/r/lib/libcolamd.so.2 (0x00007fd55c46d000)
libccolamd.so.2 => /home/ubuntu/dev/freefem/install/ff-petsc/r/lib/libccolamd.so.2 (0x00007fd55c45f000)
libcamd.so.2 => /home/ubuntu/dev/freefem/install/ff-petsc/r/lib/libcamd.so.2 (0x00007fd55c451000)
libmetis.so => /home/ubuntu/dev/freefem/install/ff-petsc/r/lib/libmetis.so (0x00007fd55c3df000)
liblapack.so.3 => /usr/lib/x86_64-linux-gnu/liblapack.so.3 (0x00007fd55bd3b000)
libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007fd55bd16000)
libgfortran.so.5 => /usr/lib/x86_64-linux-gnu/libgfortran.so.5 (0x00007fd55ba4e000)
/lib64/ld-linux-x86-64.so.2 (0x00007fd55dd39000)
libquadmath.so.0 => /usr/lib/x86_64-linux-gnu/libquadmath.so.0 (0x00007fd55ba04000)
marchywka@happy:/home/documents/cpp/proj/freefem/forum$
.
I think its not about how I use the binaries, instead, I could not configure this developer version correctly. When I run ./configure at the very end I see this error message
config.status: error: Something went wrong bootstrapping makefile fragments
for automatic dependency tracking. If GNU make was not used, consider
re-running the configure script with MAKE=“gmake” (or whatever is
necessary). You can also try re-running configure with the
‘–disable-dependency-tracking’ option to at least be able to build
the package (albeit without support for automatic dependency tracking).
See `config.log’ for more details
@prj I have also followed suggestions in this discussion FreeFem++ PETSc configuration problem in Linux - #13 by vaalea
but same error persists
Yes, you need to go past the first configure error. I have no idea where it’s coming from without the full log.
I did try uploading the log but I am new user and I am not allowed it seems.
I changed the permission on your account, you should be able to do it now.
config.log (159.3 KB)
Thank you, here it is.
Clearly, these flags are not the one from the tutorial I sent earlier. Please try with these ones instead.
Also, you probably messed up your system by installing things in / instead of a meaningful directory, so I would start from a clean VM. Also, there is nothing wrong with this config.log, so you just need to continue with the installation process (but I would start over because that --prefix=/ flag is just a very bad idea).
I agree that I might be messed my system because I tried too many things. I will start over.
@prj started over, followed exact commands from presentation shared before.
changed --prefix=/ to --prefix=${pwd} .
config (1).log (160.7 KB)
I passed the ./configure --enable-download --without-hdf5
–prefix=${PWD} stage but during make petsc-slepc have attached error. Before following the suggestion at error message to not to mess up again, wanted to write here.
You are still using an empty prefix. Set a value to something meaningful. I don’t see any PETSc error as well…
@prj
config (2).log (157.6 KB)
created a folder named fem and passed the ./configure --enable-download --without-hdf5
–prefix=/home/fem with no issues. When I do now
cd 3rdparty/ff-petsc
make petsc-slepc
I see the attached error