# How to create mesh from levet set function **URL:** \ **Category:** General Discussion\ **Created:** [September 3, 2023, 7:18pm UTC](https://community.freefem.org/t/how-to-create-mesh-from-levet-set-function/2680 "2023-09-03T19:18:34Z")\ **Posts on this page:** 20\ **Page:** 2
**Author:** ![gurkanceren](https://yyz2.discourse-cdn.com/flex030/user_avatar/community.freefem.org/gurkanceren/32/1893_2.png) [@gurkanceren](https://community.freefem.org/u/gurkanceren)\ **Post date:** [September 6, 2023, 4:29pm UTC](https://community.freefem.org/t/how-to-create-mesh-from-levet-set-function/2680/22 "2023-09-06T16:29:48Z")
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? ---
**Author:** ![prj](https://avatars.discourse-cdn.com/v4/letter/p/ecae2f/32.png) [@prj](https://community.freefem.org/u/prj)\ **Post date:** [September 6, 2023, 4:31pm UTC](https://community.freefem.org/t/how-to-create-mesh-from-levet-set-function/2680/23 "2023-09-06T16:31:57Z")
You are not typing the proper command on your machine, probably missing space, or extra new line, or something. ---
**Author:** ![gurkanceren](https://yyz2.discourse-cdn.com/flex030/user_avatar/community.freefem.org/gurkanceren/32/1893_2.png) [@gurkanceren](https://community.freefem.org/u/gurkanceren)\ **Post date:** [September 6, 2023, 4:34pm UTC](https://community.freefem.org/t/how-to-create-mesh-from-levet-set-function/2680/24 "2023-09-06T16:34:36Z")
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. ---
**Author:** ![prj](https://avatars.discourse-cdn.com/v4/letter/p/ecae2f/32.png) [@prj](https://community.freefem.org/u/prj)\ **Post date:** [September 6, 2023, 4:38pm UTC](https://community.freefem.org/t/how-to-create-mesh-from-levet-set-function/2680/25 "2023-09-06T16:38:19Z")
Do not copy/paste, type in full. Depending on your PDF viewer, some characters may not be copy/paste’d correctly, e.g., `--` becomes `–`. ---
**Author:** ![gurkanceren](https://yyz2.discourse-cdn.com/flex030/user_avatar/community.freefem.org/gurkanceren/32/1893_2.png) [@gurkanceren](https://community.freefem.org/u/gurkanceren)\ **Post date:** [September 6, 2023, 4:40pm UTC](https://community.freefem.org/t/how-to-create-mesh-from-levet-set-function/2680/26 "2023-09-06T16:40:14Z")
you are right, that was actually the problem. ---
**Author:** ![gurkanceren](https://yyz2.discourse-cdn.com/flex030/user_avatar/community.freefem.org/gurkanceren/32/1893_2.png) [@gurkanceren](https://community.freefem.org/u/gurkanceren)\ **Post date:** [September 7, 2023, 2:34pm UTC](https://community.freefem.org/t/how-to-create-mesh-from-levet-set-function/2680/27 "2023-09-07T14:34:46Z")
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, ---
**Author:** ![prj](https://avatars.discourse-cdn.com/v4/letter/p/ecae2f/32.png) [@prj](https://community.freefem.org/u/prj)\ **Post date:** [September 7, 2023, 2:46pm UTC](https://community.freefem.org/t/how-to-create-mesh-from-levet-set-function/2680/28 "2023-09-07T14:46:12Z")
What error do you get? “None works” is not a very informative message… ---
**Author:** ![marchywka](https://avatars.discourse-cdn.com/v4/letter/m/ee59a6/32.png) [@marchywka](https://community.freefem.org/u/marchywka)\ **Post date:** [September 7, 2023, 2:48pm UTC](https://community.freefem.org/t/how-to-create-mesh-from-levet-set-function/2680/29 "2023-09-07T14:48:47Z")
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. ```auto 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$ ``` . ---
**Author:** ![gurkanceren](https://yyz2.discourse-cdn.com/flex030/user_avatar/community.freefem.org/gurkanceren/32/1893_2.png) [@gurkanceren](https://community.freefem.org/u/gurkanceren)\ **Post date:** [September 7, 2023, 3:25pm UTC](https://community.freefem.org/t/how-to-create-mesh-from-levet-set-function/2680/30 "2023-09-07T15:25:26Z")
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 ---
**Author:** ![gurkanceren](https://yyz2.discourse-cdn.com/flex030/user_avatar/community.freefem.org/gurkanceren/32/1893_2.png) [@gurkanceren](https://community.freefem.org/u/gurkanceren)\ **Post date:** [September 7, 2023, 8:21pm UTC](https://community.freefem.org/t/how-to-create-mesh-from-levet-set-function/2680/31 "2023-09-07T20:21:56Z")
@prj I have also followed suggestions in this discussion [FreeFem++ PETSc configuration problem in Linux - #13 by vaalea](https://community.freefem.org/t/freefem-petsc-configuration-problem-in-linux/542/13) but same error persists ---
**Author:** ![prj](https://avatars.discourse-cdn.com/v4/letter/p/ecae2f/32.png) [@prj](https://community.freefem.org/u/prj)\ **Post date:** [September 8, 2023, 6:08am UTC](https://community.freefem.org/t/how-to-create-mesh-from-levet-set-function/2680/32 "2023-09-08T06:08:06Z")
Yes, you need to go past the first configure error. I have no idea where it’s coming from without the full log. ---
**Author:** ![gurkanceren](https://yyz2.discourse-cdn.com/flex030/user_avatar/community.freefem.org/gurkanceren/32/1893_2.png) [@gurkanceren](https://community.freefem.org/u/gurkanceren)\ **Post date:** [September 8, 2023, 6:22am UTC](https://community.freefem.org/t/how-to-create-mesh-from-levet-set-function/2680/33 "2023-09-08T06:22:45Z")
I did try uploading the log but I am new user and I am not allowed it seems. ---
**Author:** ![prj](https://avatars.discourse-cdn.com/v4/letter/p/ecae2f/32.png) [@prj](https://community.freefem.org/u/prj)\ **Post date:** [September 8, 2023, 6:29am UTC](https://community.freefem.org/t/how-to-create-mesh-from-levet-set-function/2680/34 "2023-09-08T06:29:41Z")
I changed the permission on your account, you should be able to do it now. ---
**Author:** ![gurkanceren](https://yyz2.discourse-cdn.com/flex030/user_avatar/community.freefem.org/gurkanceren/32/1893_2.png) [@gurkanceren](https://community.freefem.org/u/gurkanceren)\ **Post date:** [September 8, 2023, 6:32am UTC](https://community.freefem.org/t/how-to-create-mesh-from-levet-set-function/2680/36 "2023-09-08T06:32:40Z")
[config.log](https://community.freefem.org/uploads/short-url/pngZsQITZGGv7ITsTGq4q4DD7cq.log) (159.3 KB) Thank you, here it is. ---
**Author:** ![prj](https://avatars.discourse-cdn.com/v4/letter/p/ecae2f/32.png) [@prj](https://community.freefem.org/u/prj)\ **Post date:** [September 8, 2023, 6:45am UTC](https://community.freefem.org/t/how-to-create-mesh-from-levet-set-function/2680/37 "2023-09-08T06:45:27Z")
Clearly, these flags are not the one from the tutorial I sent earlier. Please try with these ones instead. ---
**Author:** ![prj](https://avatars.discourse-cdn.com/v4/letter/p/ecae2f/32.png) [@prj](https://community.freefem.org/u/prj)\ **Post date:** [September 8, 2023, 6:47am UTC](https://community.freefem.org/t/how-to-create-mesh-from-levet-set-function/2680/38 "2023-09-08T06:47:22Z")
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). ---
**Author:** ![gurkanceren](https://yyz2.discourse-cdn.com/flex030/user_avatar/community.freefem.org/gurkanceren/32/1893_2.png) [@gurkanceren](https://community.freefem.org/u/gurkanceren)\ **Post date:** [September 8, 2023, 6:52am UTC](https://community.freefem.org/t/how-to-create-mesh-from-levet-set-function/2680/39 "2023-09-08T06:52:47Z")
I agree that I might be messed my system because I tried too many things. I will start over. ---
**Author:** ![gurkanceren](https://yyz2.discourse-cdn.com/flex030/user_avatar/community.freefem.org/gurkanceren/32/1893_2.png) [@gurkanceren](https://community.freefem.org/u/gurkanceren)\ **Post date:** [September 8, 2023, 8:03am UTC](https://community.freefem.org/t/how-to-create-mesh-from-levet-set-function/2680/40 "2023-09-08T08:03:45Z")
@prj started over, followed exact commands from presentation shared before. changed --prefix=/ to --prefix=${pwd} . [config (1).log](https://community.freefem.org/uploads/short-url/9RwbESMsKwuvKnFimRLDhf5vdld.log) (160.7 KB) I passed the ./configure --enable-download --without-hdf5 –prefix=${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. ---
**Author:** ![prj](https://avatars.discourse-cdn.com/v4/letter/p/ecae2f/32.png) [@prj](https://community.freefem.org/u/prj)\ **Post date:** [September 8, 2023, 8:18am UTC](https://community.freefem.org/t/how-to-create-mesh-from-levet-set-function/2680/41 "2023-09-08T08:18:41Z")
You are still using an empty prefix. Set a value to something meaningful. I don’t see any PETSc error as well… ---
**Author:** ![gurkanceren](https://yyz2.discourse-cdn.com/flex030/user_avatar/community.freefem.org/gurkanceren/32/1893_2.png) [@gurkanceren](https://community.freefem.org/u/gurkanceren)\ **Post date:** [September 8, 2023, 11:08am UTC](https://community.freefem.org/t/how-to-create-mesh-from-levet-set-function/2680/42 "2023-09-08T11:08:28Z")
@prj [config (2).log](https://community.freefem.org/uploads/short-url/ygYJeLRy3IHX748Esn1IiA1N1bK.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 [Previous page](https://community.freefem.org/t/how-to-create-mesh-from-levet-set-function/2680.md?page=1) [Next page](https://community.freefem.org/t/how-to-create-mesh-from-levet-set-function/2680.md?page=3)