cannot find fftw3d and fftw3f header files. #560
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EMAN2 is nowdesigned to be built with Anaconda-provided dependencies:
https://blake.bcm.edu/emanwiki/EMAN2/Install/SourceInstall
There are no problems with those instructions that I'm aware of. We provide one single build strategy known to work on multiple platforms.
If trying to build using other sources for dependencies, I suggest doing a test compile using the supported strategy, then comparing against your attempted build to resolve issues. The reason we switched to a single compile strategy was due to limited manpower to support problems people might encounter using diverse strategies.
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Steven Ludtke, ***@***.***
On Mar 6, 2023, at 12:24 PM, xinyuan.song ***@***.***> wrote:
I am getting an error when trying to make the file because it cannot find the packages for fftw3d and fftw3f. The fftw3 package available online at MIT no longer includes these two header files. What version of this package should I be using and where can I find it?
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I followed the instructions in this link. Unfortunately, the link did not provide any useful information. The software needs to be compiled from source. During the make process, I require various C dependencies packages, which are not readily available. |
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All of the dependencies are downloaded into the Anaconda/Miniconda environment by this line:
mamba create -n eman2 eman-deps=33.1 -c cryoem -c conda-forge
If you follow the instructions step by step you will have a version compiled from source, with all dependencies installed.
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Steven Ludtke, ***@***.***
On Mar 6, 2023, at 1:52 PM, xinyuan.song ***@***.***> wrote:
I followed the instructions in this link. Unfortunately, the link did not provide any useful information. The software needs to be compiled from source. During the make process, I require various C dependencies packages, which are not readily available.
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Unfortunately, I followed this installation process exactly as it was outlined. The installation required manual installation of many C dependencies such as boost-1.7 package, hdf5=1.2 package, and fftw3 package. The versions also had to be exact, and it took me a lot of time to figure out which versions of these C packages were needed. I installed these manually, but I was unable to find fftw3d and fftw3f. |
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That process requires no external dependencies at all, other than the NVidia drivers if you are going to use deep learning. Did you remember to activate the Anaconda environment prior to running cmake? Again,
mamba create -n eman2 eman-deps=33.1 -c cryoem -c conda-forge
installs _all_ necessary dependencies with the header files, etc. You have to say "conda activate eman2" before running cmake or it won't see the dependencies. What OS platform/version are you compiling on?
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Steven Ludtke, ***@***.***
On Mar 6, 2023, at 2:05 PM, xinyuan.song ***@***.***> wrote:
Unfortunately, I followed this installation process exactly as it was outlined. The installation required manual installation of many C dependencies such as boost-1.7 package, hdf5=1.2 package, and fftw3 package. The versions also had to be exact, and it took me a lot of time to figure out which versions of these C packages were needed. I installed these manually, but I was unable to find fftw3d and fftw3f.
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I wanted to bring to your attention an issue I have been experiencing with cmake. Specifically, I am receiving the error message "Cmake could not find Boost." However, I was able to resolve this issue by manually installing boost-1.7. Subsequently, I encountered another error message indicating that "Cmake could not find xxdevs package." Fortunately, I was able to resolve this issue by installing the missing package. However, I then encountered yet another error message stating that "Cmake could not find hdf5." After installing hdf5-1.2, I was able to resolve this issue as well. I then encountered yet another error message stating that "Cmake could not find fftw." After installing fftw-3, I was able to resolve this issue as well. Specifically, I am receiving the error message "Cmake could not find fftw3d and fftw3f." I have not been able to locate these packages and I do not believe this is an issue with conda. I tested this hypothesis by conducting an experiment with a clean conda environment, and found that the issue was indeed related to Boost. After reinstalling Boost, I was able to resolve the issue. I am reaching out to you in the hopes that you may have some insight into how I can resolve the issue with fftw3d and fftw3f. Any guidance or advice you can offer would be greatly appreciated. Thank you for your time and attention to this matter! |
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Hi. Sorry you're having issues. You should not encounter any such problems when building from source using an Anaconda environment, because all of these requirements should be installed by Anaconda with the correct (tested) version of each, and cmake should not try to use system-installed libraries at all.
The solution is not to install other libraries yourself (which may be of incompatible versions or cause issues for other packages installed on your computer) but to understand why it isn't finding the Anaconda installed packages. Here is a sequence you can use to help debug the problem:
conda activate eman2 # should return a prompt starting with (eman2)
echo $LD_LIBRARY_PATH # should return a blank line. If not, unset this variable, and try cmake again
conda list # check to make sure each of the packages cmake complains about is installed. If not, something probably went wrong when installing eman-deps with conda/mamba
if this doesn't resolve the problem, please let us know what platform you are building on (Linux, Mac, WSL) and what OS version/release you are using. The full output of 'conda list' would also be useful.
cheers
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Steven Ludtke, Ph.D. ***@***.***> Baylor College of Medicine
Charles C. Bell Jr., Professor of Structural Biology Dept. of Biochemistry
Deputy Director, Advanced Technical Cores and Molecular Biology
Academic Director, CryoEM Core
Co-Director CIBR Center
On Mar 6, 2023, at 3:23 PM, xinyuan.song ***@***.***> wrote:
I wanted to bring to your attention an issue I have been experiencing with cmake. Specifically, I am receiving the error message "Cmake could not find Boost." However, I was able to resolve this issue by manually installing boost-1.7.
Subsequently, I encountered another error message indicating that "Cmake could not find xxdevs package." Fortunately, I was able to resolve this issue by installing the missing package.
However, I then encountered yet another error message stating that "Cmake could not find hdf5." After installing hdf5-1.2, I was able to resolve this issue as well.
I then encountered yet another error message stating that "Cmake could not find fftw." After installing fftw-3, I was able to resolve this issue as well.
It is crucial that the correct versions are installed, and I spent a considerable amount of time figuring out the appropriate versions of these C packages.
Specifically, I am receiving the error message "Cmake could not find fftw3d and fftw3f." I have not been able to locate these packages and I do not believe this is an issue with conda.
I tested this hypothesis by conducting an experiment with a clean conda environment, and found that the issue was indeed related to Boost. After reinstalling Boost, I was able to resolve the issue.
I am reaching out to you in the hopes that you may have some insight into how I can resolve the issue with fftw3d and fftw3f. Any guidance or advice you can offer would be greatly appreciated.
Thank you for your time and attention to this matter!
image<https://user-images.githubusercontent.com/99458242/223233998-8a618663-d5cf-4c22-a6fb-77ef555d3f82.png>
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What is the link of the instructions you are following?
On Mon, Mar 6, 2023 at 3:23 PM xinyuan.song ***@***.***> wrote:
I wanted to bring to your attention an issue I have been experiencing with
cmake. Specifically, I am receiving the error message "Cmake could not find
Boost." However, I was able to resolve this issue by manually installing
boost-1.7.
Subsequently, I encountered another error message indicating that "Cmake
could not find xxdevs package." Fortunately, I was able to resolve this
issue by installing the missing package.
However, I then encountered yet another error message stating that "Cmake
could not find hdf5." After installing hdf5-1.2, I was able to resolve this
issue as well.
I then encountered yet another error message stating that "Cmake could not
find fftw." After installing fftw-3, I was able to resolve this issue as
well.
It is crucial that the correct versions are installed, and I spent a
considerable amount of time figuring out the appropriate versions of these
C packages.
Specifically, I am receiving the error message "Cmake could not find
fftw3d and fftw3f." I have not been able to locate these packages and I do
not believe this is an issue with conda.
I tested this hypothesis by conducting an experiment with a clean conda
environment, and found that the issue was indeed related to Boost. After
reinstalling Boost, I was able to resolve the issue.
I am reaching out to you in the hopes that you may have some insight into
how I can resolve the issue with fftw3d and fftw3f. Any guidance or advice
you can offer would be greatly appreciated.
Thank you for your time and attention to this matter!
image
<https://user-images.githubusercontent.com/99458242/223233998-8a618663-d5cf-4c22-a6fb-77ef555d3f82.png>
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shadow_walker
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Where exactly does it mention boost 1.7 or hdf5 1.2?
On Mon, Mar 6, 2023 at 3:49 PM xinyuan.song ***@***.***> wrote:
https://blake.bcm.edu/emanwiki/EMAN2/Install/SourceInstall
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shadow_walker
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Can you follow the instructions posted under section “Reporting Problems”
and provide a script of commands and output of your installation steps?
On Mon, Mar 6, 2023 at 3:51 PM shadow walker ***@***.***>
wrote:
Where exactly does it mention boost 1.7 or hdf5 1.2?
On Mon, Mar 6, 2023 at 3:49 PM xinyuan.song ***@***.***>
wrote:
> https://blake.bcm.edu/emanwiki/EMAN2/Install/SourceInstall
>
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> <#560 (comment)>, or
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shadow_walker
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I tried many times from Boost-1.1, from hdf-1.0 to 2.0 and finally this two versions allowed me to go on. |
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Can you follow the instructions posted under section “Reporting Problems”
and provide a script of commands and output of your installation steps?
On Mon, Mar 6, 2023 at 3:55 PM xinyuan.song ***@***.***> wrote:
I tried many times from Boost-1.1, from hdf-1.0 to 2.0 and finally this
two versions allowed me to go on.
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I am getting an error when trying to make the file because it cannot find the packages for fftw3d and fftw3f. The fftw3 package available online at MIT no longer includes these two header files. What version of this package should I be using and where can I find it?
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