Dear David,
That suggestion did work and I got past the miniconda installation.
But now I'm getting an error related to bison for which I tried using conda
to install bison, but that also gave me permission related errors since by
default it tried to install packages where I don't have write permissions
on the cluster.
Is it possible to give global instructions in run_cmake file so that
everything is installed/downloaded where I have write permission?
Else it is likely to give other permission errors during multiple steps
that it might be doing under-the-hood.
Looking forward to your valuable suggestions. thank you and best regards,
Vaibhav
removing gmp-6.2.1-h58526e2_0
-- Miniconda install successful!
-- Checking for Python package numpy -- found
-- Checking for Python package scipy -- found
-- Checking for Python package matplotlib -- found
-- Checking for Python package setuptools -- found
-- Checking for Python package tkinter -- found
-- Checking for Python package distutils.sysconfig -- found
-- Python relative site-packages location:
<prefix>/lib/python3.9/site-packages
CMake Error at
/home/opt_ohpc_pub/utils/cmake/3.14.3/share/cmake-3.14/Modules/FindPackageHandleStandardArgs.cmake:137
(message):
Could NOT find BISON (missing: BISON_EXECUTABLE)
Call Stack (most recent call first):
/home/opt_ohpc_pub/utils/cmake/3.14.3/share/cmake-3.14/Modules/FindPackageHandleStandardArgs.cmake:378
(_FPHSA_FAILURE_MESSAGE)
/home/opt_ohpc_pub/utils/cmake/3.14.3/share/cmake-3.14/Modules/FindBISON.cmake:290
(FIND_PACKAGE_HANDLE_STANDARD_ARGS)
cmake/ExternalPrograms.cmake:23 (find_package)
CMakeLists.txt:123 (include)
-- Configuring incomplete, errors occurred!
See also
"/scratch/vaibhavdixit.bitspilani/amber20_src/build/CMakeFiles/CMakeOutput.log".
See also
"/scratch/vaibhavdixit.bitspilani/amber20_src/build/CMakeFiles/CMakeError.log".
If the cmake build report looks OK, you should now do the following:
make install
source /scratch/vaibhavdixit.bitspilani/amber20/amber.sh
Consider adding the last line to your login startup script, e.g. ~/.bashrc
[vaibhavdixit.bitspilani.login4 build]$ conda install -c conda-forge bison
flex
Collecting package metadata (current_repodata.json): done
Solving environment: done
==> WARNING: A newer version of conda exists. <==
current version: 4.8.3
latest version: 4.11.0
Please update conda by running
$ conda update -n base -c defaults conda
## Package Plan ##
environment location: /home/apps/bio_tools/conda
added / updated specs:
- bison
- flex
The following packages will be downloaded:
package | build
---------------------------|-----------------
bison-3.7.5 | h2531618_1 708 KB
ca-certificates-2021.10.8 | ha878542_0 139 KB
conda-forge
certifi-2021.10.8 | py37h89c1867_1 145 KB
conda-forge
conda-4.11.0 | py37h89c1867_0 16.9 MB
conda-forge
flex-2.6.4 | h58526e2_1004 330 KB
conda-forge
m4-1.4.18 | h516909a_1001 172 KB
conda-forge
openssl-1.1.1l | h7f8727e_0 2.5 MB
python_abi-3.7 | 2_cp37m 4 KB
conda-forge
------------------------------------------------------------
Total: 20.9 MB
The following NEW packages will be INSTALLED:
bison pkgs/main/linux-64::bison-3.7.5-h2531618_1
flex conda-forge/linux-64::flex-2.6.4-h58526e2_1004
m4 conda-forge/linux-64::m4-1.4.18-h516909a_1001
python_abi conda-forge/linux-64::python_abi-3.7-2_cp37m
The following packages will be UPDATED:
ca-certificates pkgs/main::ca-certificates-2020.6.24-0 -->
conda-forge::ca-certificates-2021.10.8-ha878542_0
certifi intel::certifi-2019.11.28-py37_0 -->
conda-forge::certifi-2021.10.8-py37h89c1867_1
conda pkgs/main::conda-4.8.3-py37_0 -->
conda-forge::conda-4.11.0-py37h89c1867_0
openssl intel::openssl-1.1.1d-1 -->
pkgs/main::openssl-1.1.1l-h7f8727e_0
Proceed ([y]/n)? y
Downloading and Extracting Packages
conda-4.11.0 | 16.9 MB |
########################################################################################################################################################
| 100%
openssl-1.1.1l | 2.5 MB |
########################################################################################################################################################
| 100%
python_abi-3.7 | 4 KB |
########################################################################################################################################################
| 100%
bison-3.7.5 | 708 KB |
########################################################################################################################################################
| 100%
certifi-2021.10.8 | 145 KB |
########################################################################################################################################################
| 100%
flex-2.6.4 | 330 KB |
########################################################################################################################################################
| 100%
m4-1.4.18 | 172 KB |
########################################################################################################################################################
| 100%
ca-certificates-2021 | 139 KB |
########################################################################################################################################################
| 100%
Preparing transaction: done
Verifying transaction: failed
EnvironmentNotWritableError: The current user does not have write
permissions to the target environment.
environment location: /home/apps/bio_tools/conda
uid: 5504
gid: 5504
Regards,
Dr. Vaibhav A. Dixit,
Asst. Prof., Department of Medicinal Chemistry,
National Institute of Pharmaceutical Education and Research, Guwahati
(NIPER-G), Sila Katamur (Halugurisuk), P.O.: Changsari, Dist: Kamrup, Pin:
781101, Assam, India
Mob. No. +91-7709129400,
Email: vaibhav.niperguwahati.in; vaibhavadixit.gmail.com
https://niperguwahati.ac.in/DOC/profile/dixit.pdf
https://www.linkedin.com/in/vaibhav-dixit-b1a07a39/
ORCID ID: https://orcid.org/0000-0003-4015-2941
NCBI bibliography:
https://www.ncbi.nlm.nih.gov/myncbi/1Jgo56b26_AYKd/bibliography/public/
http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra
Please consider the environment before printing this e-mail
On Thu, Dec 16, 2021 at 7:19 PM David A Case <david.case.rutgers.edu> wrote:
> On Thu, Dec 16, 2021, Vaibhav Dixit wrote:
>
> >-- Using cached Miniconda installer at
>
> >/scratch/vaibhavdixit.bitspilani/amber20_src/build/CMakeFiles/miniconda/download/Miniconda3-latest-Linux-x86_64.sh
>
> >error while loading shared libraries: libz.so.1: failed to map segment
> from
> >shared object: Operation not permitted
>
> Here is a relevant Google hit:
>
>
> https://stackoverflow.com/questions/60106630/conda-exe-error-while-loading-shared-libraries-libz-so-1
>
> Basically, it seems likely that your /tmp folder has odd permissions. Try
> the fixes suggested in the above post.
>
> ....dac
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Dec 16 2021 - 20:30:03 PST
