Fix updated Rstudio interactive app error on GPU nodes

assigned to @louistw

# From /home/louistw/.local/share/rstudio/log/rserver.log on pascalnodes:

2023-09-27T18:42:39.400971Z [rserver] ERROR R did not return any output when queried for directory location information; LOGGED FROM: bool rstudio::core::r_util::{anonymous}::detectRLocationsUsingR(const string&, rstudio::core::FilePath*, rstudio::core::FilePath*, rstudio::core::config_utils::Variables*, std::string*, const string&, const string&, const rstudio::core::FilePath&) src/cpp/core/r_util/REnvironmentPosix.cpp:538
2023-09-27T18:42:39.613641Z [rserver] ERROR system error 71 (Protocol error) [description: Unable to parse version from R, version-info: , r-error: ]; OCCURRED AT rstudio::core::Error rstudio::core::r_util::rVersion(const rstudio::core::FilePath&, const rstudio::core::FilePath&, const string&, const string&, const string&, const rstudio::core::FilePath&, std::string*) src/cpp/core/r_util/REnvironmentPosix.cpp:946; LOGGED FROM: bool rstudio::core::r_util::detectREnvironment(const rstudio::core::FilePath&, const rstudio::core::FilePath&, const string&, std::string*, std::string*, rstudio::core::r_util::EnvironmentVars*, std::string*, const string&, const string&, const rstudio::core::FilePath&) src/cpp/core/r_util/REnvironmentPosix.cpp:789
2023-09-27T18:43:08.856219Z [rserver] ERROR system error 111 (Connection refused) [request-uri: /rpc/client_init]; OCCURRED AT void rstudio::core::http::LocalStreamAsyncClient::handleConnect(const rstudio_boost::system::error_code&) src/cpp/server/ServerSessionProxy.cpp:124; LOGGED FROM: void rstudio::server::session_proxy::{anonymous}::logIfNotConnectionTerminated(const rstudio::core::Error&, const rstudio::core::http::Request&) src/cpp/server/ServerSessionProxy.cpp:477

I tried a command from this post, and got the following error:

# On pascalnodes partition(c0107)
$ R --slave --vanilla -e 'cat(R.Version()$major,R.Version()$minor, sep=".")'

[1]    27248 illegal hardware instruction  R --slave --vanilla -e 'cat(R.Version()$major,R.Version()$minor, sep=".")'

# On short partition(c1068):
$ R --slave --vanilla -e 'cat(R.Version()$major,R.Version()$minor, sep=".")'
4.2.0%

Building R-4.2.2-foss-2022b-bare.eb on pascalnodes to see if it can solve the problem.

R/4.2.2-foss-2022b module is now available. Tested the R App with the new module and it works.

Do we want to rebuild old versions? @ravi89

From /share/apps/rc/software/R/4.2.0-foss-2021a-bare/easybuild/easybuild-R-4.2.0-20220719.170517.log:

== 2022-07-19 16:55:40,855 easyblock.py:303 INFO This is EasyBuild 4.5.5 (framework: 4.5.5, easyblocks: 4.5.5) on host c0115

Node c0115 is intel-dcb partition. We can go ahead and rebuild R/4.2.0-foss-2021a-bare in pascalnodes and see if this resolve the issue.

while building, got the following error:

== 2023-10-16 13:54:41,012 build_log.py:171 ERROR EasyBuild crashed with an error 
(at easybuild/software/EasyBuild/4.8.1/lib/python2.7/site-packages/easybuild/base/exceptions.py:126 in __init__): 
OpenSSL v1.1 headers not found in host system, but libraries for v1.1.1k are present. Install the 
development package of OpenSSL for your system or force building OpenSSL from source in EasyBuild by 
setting 'wrap_system_openssl = False' in the OpenSSL easyconfig. (at 
easybuild/software/EasyBuild/4.8.1/lib/python2.7/site-packages/easybuild/easyblocks/o/openssl_wrapper.py:267 in __init__)

Check installed yum packages and found that we have mix versions installed but only one version of devel package installed:

$ yum list installed| grep openssl
Skipping unreadable repository '/etc/yum.repos.d/cm.repo'
cm-openssl.x86_64            1.1.1l-100108_cm8.2_b4a5310276
openssl.x86_64               1:1.0.2k-26.el7_9      @rhel-7-server-rpms
openssl-devel.x86_64         1:1.0.2k-26.el7_9      @rhel-7-server-rpms
openssl-libs.x86_64          1:1.0.2k-26.el7_9      @rhel-7-server-rpms
openssl098e.x86_64           0.9.8e-29.el7_2.3      @rhel-7-server-rpms
openssl11.x86_64             1:1.1.1k-5.el7         @epel
openssl11-libs.x86_64        1:1.1.1k-5.el7         @epel
xmlsec1-openssl.x86_64       1.2.20-7.el7_4         @rhel-7-server-rpms

added Sprint 23-21 label and removed Sprint 23-20 label

First, go through easybuild log files and get the package name and which host it was built on.

$ for f in /share/apps/rc/software/*/*/easybuild/*.log; do
echo $f | awk -F '/' '{print $6"/"$7}' >> package-hosts.txt;
head -n 1 $f | perl -lne 'print $1 if /(\S+).$/' >> package-hosts.txt;
done

Then count how many different hosts with:

$ grep -vP "'|/" package-hosts.txt| sort | uniq -c
     43 c0001
     49 c0002
     16 c0003
     32 c0004
     60 c0005
     20 c0006
     22 c0007
     65 c0008
     31 c0009
      2 c0010
      3 c0011
      9 c0012
     15 c0013
      6 c0014
     29 c0015
     15 c0016
      2 c0017
     35 c0018
      4 c0019
     36 c0020
      4 c0021
     11 c0022
     10 c0023
     22 c0024
      8 c0025
     11 c0027
      9 c0028
      9 c0030
      4 c0031
      7 c0032
      5 c0033
     26 c0034
     55 c0035
     10 c0036
     11 c0037
      4 c0038
     15 c0039
      9 c0040
     24 c0041
     20 c0042
     10 c0043
      7 c0044
      1 c0045
     52 c0046
     15 c0047
     57 c0048
      1 c0050
     26 c0051
      2 c0052
      2 c0053
      3 c0054
      1 c0055
      6 c0056
     20 c0057
      4 c0058
      2 c0059
     18 c0060
      2 c0061
      2 c0062
     82 c0063
      5 c0064
     27 c0065
      1 c0066
     98 c0067
      5 c0068
     22 c0069
     13 c0070
      3 c0071
     16 c0073
      4 c0074
      2 c0075
      2 c0076
     14 c0077
     16 c0078
     15 c0079
     14 c0080
     12 c0081
     22 c0082
      3 c0083
      3 c0084
      1 c0085
      1 c0086
     11 c0087
     26 c0088
     23 c0089
     81 c0090
      7 c0091
     23 c0092
     23 c0093
     36 c0094
     66 c0095
     37 c0096
     15 c0097
     19 c0098
      3 c0099
     13 c0100
     18 c0101
      9 c0103
     82 c0104
     64 c0105
     34 c0106
     72 c0107
     18 c0108
     13 c0109
      1 c0110
     96 c0111
     14 c0112
     62 c0113
     11 c0114
      9 c0115
     16 c0116
     68 c0118
      2 c0119
      1 c0121
     16 c0122
      1 c0124
      8 c0126
      1 c0129
     44 c0132
     18 c0134
      9 c0135
      9 c0136
      3 c0139
      1 c0146
      1 c0150
      3 c0153
      4 c0154
     85 c0158
      1 c0164
      1 c0166
      4 c0171
      6 c0178
      1 c0183
      4 c0186
      3 c0187
      1 c0188
      1 c0201
      4 c0202
      8 c0203
      1 c0208
     18 c0209
      3 c0213
      2 c0218
      7 c0220
      1 c0223
      3 c0225
      4 c0228
      7 c0229
      1 c0234
      1 cheaha-master02
    374 login001
     11 login004
     66 shealy001
      2 shealy002
     74 shealy005
     18 shealy006
     45 shealy007
      3 shealy008
      2 shealy009
      1 shealy012
      2 shealy013
      3 shealy021
     13 shealy029
     13 shealy033
      8 shealy034
      6 shealy035
     21 shealy036
      4 shealy037
      8 shealy038
      2 shealy039

added Sprint 23-22 label and removed Sprint 23-21 label

added Sprint 23-24 label and removed Sprint 23-22 label

mentioned in merge request !15 (merged)

added Sprint 23-25 label and removed Sprint 23-24 label

assigned to @ravi89 and unassigned @louistw

added Sprint 24-1 label and removed Sprint 23-25 label

mentioned in commit 6d287850

closed with merge request !15 (merged)

unassigned @ravi89

Fix updated Rstudio interactive app error on GPU nodes

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