libtiff.so.6 links persistently, although it's not on my system

[walidabualafia]

Hi,

I've been trying to get MotionCor3 working for the past hour, but seems like something in the makefile is not working. I am using makefile11.

Whenever I run the compilation step, it succeeds. It compiles all the necessary files, then echoes that MotionCor3 has been generated.

Now when I try to run ./MotionCor3, I get this error back:

./MotionCor3: error while loading shared libraries: libtiff.so.6: cannot open shared object file: No such file or directory

Weirdly, when I run ls /usr/lib64 | grep tiff, I see the following:

libtiff.so
libtiff.so.5
libtiff.so.5.3.0
libtiffxx.so
libtiffxx.so.5
libtiffxx.so.5.3.0

I tried specifying the path to my libtiff install manually, but it failed and threw lots and lots of compiler errors.

I'm certain I do not have libtiff.so.6 installed anywhere in my system. I manually listed and checked each path in my LD_LIBRARY_PATH. Do you know where the compiler is picking up this version of libtiff?

A quick search shows that the required version ships with Arch Linux/OpenSUSE distributions. I'm compiling on RHEL8.

Any help would be appreciated. :)

Thanks, Walid

[szhengczii]

@walidabualafia, when I run ldd on MotionCor3 executable, this is what I got: libtiff.so.6 => /home/shawn.zheng/miniconda3/lib/libtiff.so.6 (0x00007ff131667000)

This is the line in my .bashrc file: export LD_LIBRARY_PATH="$HOME/miniconda3/lib:$LD_LIBRARY_PATH"

[walidabualafia]

Hi Shawn,

Thanks for your response. I was able to get past this error by obtaining libtiff from Conda.

However, I am now running into this new error: ./MotionCor3: error while loading shared libraries: libcuda.so.1: cannot open shared object file: No such file or directory

Please note that I tried compiling with CUDA 11.0, CUDA 11.2, and CUDA 11.4 and got the same error each time. Which version of CUDA did you use?

Thanks for your help! Walid

[szhengczii]

Hi Walid,

Have you added the path to LD_LIBRARY_PATH?

Best, Shawn

On Mon, Nov 6, 2023 at 8:18 AM Walid Abu Al-Afia @.***> wrote:

Hi Shawn,

Thanks for your response. I was able to get past this error by obtaining libtiff from Conda.

However, I am now running into this new error: ./MotionCor3: error while loading shared libraries: libcuda.so.1: cannot open shared object file: No such file or directory

Please note that I tried compiling with CUDA 11.0, CUDA 11.2, and CUDA 11.4 and got the same error each time. Which version of CUDA did you use?

Thanks for your help! Walid

— Reply to this email directly, view it on GitHub https://github.com/czimaginginstitute/MotionCor3/issues/7#issuecomment-1795333344, or unsubscribe https://github.com/notifications/unsubscribe-auth/BBUDUPYS6OCVGEUKD3JGKUDYDEEW5AVCNFSM6AAAAAA6YK3CCCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTOOJVGMZTGMZUGQ . You are receiving this because you commented.Message ID: @.***>

[walidabualafia]

Yeah, it is in my LD_LIBRARY_PATH. When I check my $CUDA_HOME/lib directory, I don't have the libcuda.so.1 file. The closest thing I have is libcudart.so. I checked all versions of CUDA, never really had a problem running them with any other app. Maybe I can try to install the same CUDA version you're running. What your output for nvcc --version?

Thanks for the support, Shawn. Walid

[szhengczii]

@walidabualafia: what do you see when you run "ldd MotionCor3"? what does libcuda.so.1 point to? This is what I have. libcuda.so.1 => /lib64/libcuda.so.1 (0x00007f3c71eb1000)

Below is the output of "nvcc --version". nvcc: NVIDIA (R) Cuda compiler driver Copyright (c) 2005-2022 NVIDIA Corporation Built on Wed_Sep_21_10:33:58_PDT_2022 Cuda compilation tools, release 11.8, V11.8.89 Build cuda_11.8.r11.8/compiler.31833905_0

[walidabualafia]

@szhengczii: thanks again. My output for ldd MotionCor3 shows libcuda.so.1 => /path/to/cuda/install/lib64/libcuda.so.1 (0x0000155553647000)

My nvcc --version is 11.4. Any idea how I can get MotionCor3 running?

[szhengczii]

@walidabualafia: I guess you may have multiple cuda versions installed. I am guessing that you compiled with cuda 11.4 but do not have cuda 11.4 library added to LD_LIBRARY_PATH. What do you see when you run "echo $LD_LIBRARY_PATH"?

[walidabualafia]

@szhengczii: The only Cuda in my path is 11.4, as you can see below:

/cm/local/apps/cuda/libs/current/lib64:/cm/shared/apps/cuda11.4/toolkit/11.4.2/targets/x86_64-linux/lib:/other/apps/in/my/LD_LIBRARY_PATH

I also compiled the bin with this version of Cuda.

When I ran ldd again, I noticed that I am getting:

 libtiff.so.6 => not found

I am running on RHEL8. The version installed on my system is libtiff.so.5. Do you know where I can install this exact version of the library? I think that would be great help. I looked online, but could not find many resources to point me. I compiled AreTomo2 on the same system and it runs fine.

Thanks! :)

[walidabualafia]

Ok, I was able to get it working by installing an older libtiff from Conda. Thanks for the help! :)