Re: [AMBER] AmberTools installation issue

From: Rybenkov, Valentin V. via AMBER <>
Date: Sun, 17 Jul 2022 23:15:15 +0000

This is an update to the installation error of AmberTools22. I traced the error to a specific line in makefiles. The error involves an attempt to write into a privileged area. It occurs on line
$(MAKE) $(MAKESILENT) -f CMakeFiles/Makefile2 PerlMol
of the “# Target rules for targets named PerlMol’ of the main Makefile.
Then into the block “# Target rules for target AmberTools/src/PerlMol-0.3500/CMakeFiles/PerlMol.dir” of amber22_src/build/CMakeFiles/Makefile2.
Then into the file AmberTools/src/PerlMol-0.3500/CMakeFiles/PerlMol.dir/build.make, line “cd /home/valya/Amber22/amber22_src/build/AmberTools/src/PerlMol-0.3500/build && /usr/bin/make”,
Specifically, the instruction “/usr/bin/make” generates an error, using presumably the Makefile in $AMBERHOME/amber22_src/build/AmberTools/src/PerlMol-0.3500/build/.

I do not understand why this script tries to write into a write-protected directory. This seems to be a bug in the installation package. Is there a way to bypass it?

Valentin V. Rybenkov
University of Oklahoma
101 Stephenson Parkway
Norman, OK 73019

From: Rybenkov, Valentin V. via AMBER<>
Sent: Friday, July 15, 2022 11:35 PM
Subject: [AMBER] AmberTools installation issue

Hello everybody,

I am trying to build AmberTools22 on a CentOS 7 machine, no root privileges. I load CMake 3.20 using “module load CMake”. (I know, the Amber manual recommends installing CMake from, but that was creating a conflict with a running cmake version at the run_cmake stage). The line “./run_cmake” was executed smoothly. However, I have problems with the next line, “make install”. Early on, I am getting an error:
“[ 20%] Performing build step for 'PerlMol'
ERROR NHC: FATAL: Can't write >>/var/log/true.log 2>&1 as valya -- Read-only filesystem/device failure?

Apparently, gcc is trying to write a test file into an accessible-to-root-only partition. Is there a way to change this behavior of gcc, perhaps by changing environmental parameters?

Many thanks,

Valentin V. Rybenkov

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