GROMACS version: git repository
GROMACS modification: No
Dear all,
I’m trying to install gromacs with the drude branch from the git repository but I found a few errors I can’t solve. First, I used:
git clone git@gitlab.com:gromacs/gromacs.git
cd gromacs
git checkout drude
And got:
Branch drude set up to track remote branch drude from origin.
Switched to a new branch ‘drude’
Then I tried to compile as any other version of gromacs, but I had to add a few flags because I was getting an error about the GMX_SIMD. I ended up using:
cmake .. -DCMAKE_INSTALL_PREFIX=/home/afrs/ -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=CUDA -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda-11.2 -DCMAKE_C_COMPILER=/opt/ohpc/pub/compiler/gcc/8.3.0/bin/gcc -DCMAKE_CXX_COMPILER=/opt/ohpc/pub/compiler/gcc/8.3.0/bin/g++ -DGMX_SIMD=None -DNVML_INCLUDE_DIR=/usr/cuda/include -DCMAKE_BUILD_TYPE=Release -DNVML_LIBRARY=/usr/cuda/lib64/stubs/libnvidia-ml.so
And I got:
…
…
-- Performing Test HAS_NO_UNUSED_VARIABLE
-- Performing Test HAS_NO_UNUSED_VARIABLE - Success
-- Check if the system is big endian
-- Searching 16 bit integer
-- Searching 16 bit integer - Using unsigned short
-- Check if the system is big endian - little endian
-- Looking for inttypes.h
-- Looking for inttypes.h - found
-- Performing Test HAS_NO_UNUSED_PARAMETER
-- Performing Test HAS_NO_UNUSED_PARAMETER - Success
-- Performing Test HAS_NO_DEPRECATED_REGISTER
-- Performing Test HAS_NO_DEPRECATED_REGISTER - Success
Downloading: http://gerrit.gromacs.org/snapshot/refs/heads/master
-- [download 100% complete]
-- [download 0% complete]
CMake Error at tests/CMakeLists.txt:57 (message):
error: downloading 'http://gerrit.gromacs.org/snapshot/refs/heads/master'
failed
status_code: 22
status_string: "HTTP response code said error"
log: Trying 130.237.11.134:80...
Trying 2001:6b0:1:1191:9a03:9bff:fe1e:e668:80...
Immediate connect fail for 2001:6b0:1:1191:9a03:9bff:fe1e:e668: Network is
unreachable
Connected to gerrit.gromacs.org (130.237.11.134) port 80 (#0)
GET /snapshot/refs/heads/master HTTP/1.1
Host: gerrit.gromacs.org
User-Agent: curl/7.71.1
Accept: */*
Mark bundle as not supporting multiuse
HTTP/1.1 301 Moved Permanently
Server: nginx/1.18.0 (Ubuntu)
Date: Mon, 28 Mar 2022 07:26:27 GMT
Content-Type: text/html
Content-Length: 178
Connection: keep-alive
Location: https://gerrit.gromacs.org/snapshot/refs/heads/master
Ignoring the response-body
[178 bytes data]
Connection #0 to host gerrit.gromacs.org left intact
Issue another request to this URL:
'https://gerrit.gromacs.org/snapshot/refs/heads/master'
Trying 130.237.11.134:443...
Trying 2001:6b0:1:1191:9a03:9bff:fe1e:e668:443...
Immediate connect fail for 2001:6b0:1:1191:9a03:9bff:fe1e:e668: Network is
unreachable
Connected to gerrit.gromacs.org (130.237.11.134) port 443 (#1)
ALPN, offering h2
ALPN, offering http/1.1
TLSv1.0 (OUT), TLS header, Certificate Status (22):
[5 bytes data]
TLSv1.3 (OUT), TLS handshake, Client hello (1):
[512 bytes data]
TLSv1.2 (IN), TLS header, Certificate Status (22):
[5 bytes data]
TLSv1.3 (IN), TLS handshake, Server hello (2):
[122 bytes data]
TLSv1.2 (IN), TLS header, Finished (20):
[5 bytes data]
TLSv1.2 (IN), TLS header, Supplemental data (23):
[5 bytes data]
[1 bytes data]
TLSv1.3 (IN), TLS handshake, Encrypted Extensions (8):
[25 bytes data]
TLSv1.2 (IN), TLS header, Supplemental data (23):
[5 bytes data]
[1 bytes data]
TLSv1.3 (IN), TLS handshake, Certificate (11):
[4069 bytes data]
TLSv1.2 (IN), TLS header, Supplemental data (23):
[5 bytes data]
[1 bytes data]
TLSv1.3 (IN), TLS handshake, CERT verify (15):
[264 bytes data]
TLSv1.2 (IN), TLS header, Supplemental data (23):
[5 bytes data]
[1 bytes data]
TLSv1.3 (IN), TLS handshake, Finished (20):
[52 bytes data]
TLSv1.2 (OUT), TLS header, Finished (20):
[5 bytes data]
TLSv1.3 (OUT), TLS change cipher, Change cipher spec (1):
[1 bytes data]
TLSv1.2 (OUT), TLS header, Supplemental data (23):
[5 bytes data]
[1 bytes data]
TLSv1.3 (OUT), TLS handshake, Finished (20):
[52 bytes data]
SSL connection using TLSv1.3 / TLS_AES_256_GCM_SHA384
ALPN, server accepted to use http/1.1
Server certificate:
subject: CN=gerrit.gromacs.org
start date: Jan 23 22:34:35 2022 GMT
expire date: Apr 23 22:34:34 2022 GMT
subjectAltName: host "gerrit.gromacs.org" matched cert's "gerrit.gromacs.org"
issuer: C=US; O=Let's Encrypt; CN=R3
SSL certificate verify result: unable to get local issuer certificate (20), continuing anyway.
TLSv1.2 (OUT), TLS header, Supplemental data (23):
[5 bytes data]
[1 bytes data]
GET /snapshot/refs/heads/master HTTP/1.1
Host: gerrit.gromacs.org
User-Agent: curl/7.71.1
Accept: */*
TLSv1.2 (IN), TLS header, Supplemental data (23):
[5 bytes data]
[1 bytes data]
TLSv1.3 (IN), TLS handshake, Newsession Ticket (4):
[281 bytes data]
TLSv1.2 (IN), TLS header, Supplemental data (23):
[5 bytes data]
[1 bytes data]
TLSv1.3 (IN), TLS handshake, Newsession Ticket (4):
[281 bytes data]
old SSL session ID is stale, removing
TLSv1.2 (IN), TLS header, Supplemental data (23):
[5 bytes data]
[1 bytes data]
Mark bundle as not supporting multiuse
HTTP/1.1 403 Forbidden
Server: nginx/1.18.0 (Ubuntu)
Date: Mon, 28 Mar 2022 07:26:28 GMT
Content-Type: text/html
Content-Length: 162
Connection: keep-alive
The requested URL returned error: 403
Closing connection 1
TLSv1.2 (OUT), TLS header, Supplemental data (23):
[5 bytes data]
[1 bytes data]
TLSv1.3 (OUT), TLS alert, close notify (256):
[2 bytes data]
-- Configuring incomplete, errors occurred!
I supposed it couldn’t download the regression tests from gerrit.gromacs.org, as I saw the CMakeLists.txt in the master is updated to use:
REGRESSIONTEST_URL https://gitlab.com/gromacs/gromacs-regressiontests/-/archive/${REGRESSIONTEST_BRANCH}/gromacs-regressiontests-${REGRESSIONTEST_BRANCH}.tar.gz)
But I’m not sure if I can just replace the file in the drude branch with this one from the master.
So I downloaded the tests from the newest release and added this flag:
-DREGRESSIONTEST_PATH=/home/afrs/gromacs/regressiontests-2022
The configuration can be done, but when I use make, I get the following:
**Scanning dependencies of target mdrun_objlib**
[ 0%] Building CXX object src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/md.cpp.o
[ 0%] Building CXX object src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o
[ 0%] Building CXX object src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/membed.cpp.o
[ 0%] Building CXX object src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/repl_ex.cpp.o
[ 0%] Building CXX object src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/resource-division.cpp.o
[ 0%] Building CXX object src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/runner.cpp.o
[ 0%] Built target mdrun_objlib
**Scanning dependencies of target git-version-info**
[ 0%] **Generating git version information**
[ 0%] Built target git-version-info
[ 0%] **Generating baseversion-gen.c**
[ 1%] **Building NVCC (Device) object src/gromacs/CMakeFiles/libgromacs.dir/mdlib/nbnxn_cuda/libgromacs_generated_nbnxn_cuda.cu.o**
nvcc fatal : Unsupported gpu architecture 'compute_20'
CMake Error at libgromacs_generated_nbnxn_cuda.cu.o.Release.cmake:216 (message):
Error generating
/home/afrs/gromacs/build/src/gromacs/CMakeFiles/libgromacs.dir/mdlib/nbnxn_cuda/./libgromacs_generated_nbnxn_cuda.cu.o
make[2]: *** [src/gromacs/CMakeFiles/libgromacs.dir/mdlib/nbnxn_cuda/libgromacs_generated_nbnxn_cuda.cu.o] Error 1
make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2
make: *** [all] Error 2
…
I’m not sure whether this error is related to the fact that I used the regression tests from a released version or there is an incompatibility between the code and the hardware I’m using.
Does anyone have any suggestions on how to solve these problems?
Thank you very much!