GLIBC_2.29 on CentOS7

hsin wang

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Jan 2, 2024, 3:57:50 PM1/2/24

to NMR POKY/SPARKY USER GROUP

I installed poky on CentOS7. Thinking it is a Red Hat flavored OS, I did

sudo yum install libxcb*-devel xcb-util-*-devel libXrender-devel libxkbcommon*-devel libXi-devel libdrm-devel libXcursor-devel libXcomposite-devel libpng15

But I see the error message when I started poky.sh

--

/home/poky_linux/bin/poky: /lib64/libm.so.6: version `GLIBC_2.29' not found (required by /home/poky_linux/bin/poky)
/home/poky_linux/bin/poky: /lib64/libstdc++.so.6: version `GLIBCXX_3.4.20' not found (required by /home/poky_linux/bin/poky)
/home/poky_linux/bin/poky: /lib64/libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by /home/poky_linux/bin/poky)
/home/poky_linux/bin/poky: /lib64/libm.so.6: version `GLIBC_2.29' not found (required by /home/poky_linux/lib_linux/libpython3.7m.so.1.0)
/home/poky_linux/bin/poky: /lib64/libc.so.6: version `GLIBC_2.25' not found (required by /home/poky_linux/lib_linux/libpython3.7m.so.1.0)
/home/poky_linux/bin/poky: /lib64/libc.so.6: version `GLIBC_2.26' not found (required by /home/poky_linux/lib_linux/libpython3.7m.so.1.0)
/home/poky_linux/bin/poky: /lib64/libc.so.6: version `GLIBC_2.28' not found (required by /home/poky_linux/lib_linux/libpython3.7m.so.1.0)
/home/poky_linux/bin/poky: /lib64/libm.so.6: version `GLIBC_2.29' not found (required by /home/poky_linux/lib_linux/libtcl8.6.so)
/home/poky_linux/bin/poky: /lib64/libm.so.6: version `GLIBC_2.29' not found (required by /home/poky_linux/lib_linux/libtk8.6.so)
/home/poky_linux/bin/poky: /lib64/libc.so.6: version `GLIBC_2.26' not found (required by /home/poky_linux/lib_linux/libX11.so.6)
/home/poky_linux/bin/poky: /lib64/libm.so.6: version `GLIBC_2.29' not found (required by /home/poky_linux/lib_linux/libpng16.so.16)
/home/poky_linux/bin/poky: /lib64/libz.so.1: version `ZLIB_1.2.9' not found (required by /home/poky_linux/lib_linux/libpng16.so.16)

-

It seems all these libc, libm, libz are there but the GLIBC_2.29 versions are not available. What should I do?

Lee, Woonghee

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Jan 2, 2024, 6:45:43 PM1/2/24

to hsin wang, NMR POKY/SPARKY USER GROUP

Dear Hsin,

Two solutions. Simply CentOS 7 is too old to run POKY out of the box.

One, you can upgrade your kernel (very risky and difficult. not recommended)

Two, installl Singularity version (recommended).

--

Woonghee Lee, Ph.D.

Assistant Professor of Chemistry

University of Colorado Denver

woongh...@ucdenver.edu

https://poky.clas.ucdenver.edu

https://poky.clas.ucdenver.edu/wlee-group

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hsin wang

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Jan 12, 2024, 4:26:33 PM1/12/24

to Lee, Woonghee, NMR POKY/SPARKY USER GROUP

Thank you for writing to me. I built the singularity version. After which, there were still a few gtk issues. But most problematic is the permission problem with /run/user/1000. The /run and /run/user both have permission of 755, whereas 100? files have permission of 700. This seemed OK with other computers.

I also looked at the poky.def that I was instructed to download in order to install singularity version and found that it was written for a ubuntu platform. Do you have one written for redhat system like CentOS?

If you do, I am willing to give it another try.

Thank you,

Hsin

Lee, Woonghee

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Jan 12, 2024, 4:58:30 PM1/12/24

to hsin wang, NMR POKY/SPARKY USER GROUP

Dear Hsin,

I am wondering if the permission problem is on the centos server or the files in the container. You probably want to check if your account is also in the group of “docker” that you see in /etc/group and /etc/gshadow.

About the poky.def, it is a ubuntu container that runs on whatever host system you have. It is a virtualization technique. So it’s not the problem. You want to check with your centos server setting allowing you to run a container. I am running my poky container on my centos 7 without any problem after resolving that group issue.

Best,

Woonghee

Woonghee Lee, I.E.I.P., M.S., Ph.D.

Assistant Professor

Department of Chemistry

University of Colorado Denver

1151 Arapahoe St. (Science Bldg.) Rm 4128A (office), Rm 4128 (dry lab), Rm 4133 (wet lab)

Denver, CO 80217-3364, USA

Office: +1-303-315-7672

woongh...@ucdenver.edu

https://poky.clas.ucdenver.edu

https://poky.clas.ucdenver.edu/wlee-group