OpenCPU - Failed to set rlimit. ENOSYS - r

I already installed OpenCPU on a Ubuntu Server - Ubuntu 14.04.1 LTS (GNU/Linux 3.13.0-32-generic x86_64) - and everything worked perfectly without any problems.
Here I want to say that I really like this API and I am very thankful for all the effort from the people (I think mostly Jeroen Ooms) working on it.
Now I installed it again, but on another Server hosted at another provider. It is also a Ubuntu Server - Ubuntu 14.04.1 LTS (GNU/Linux 3.13.0-042stab093.4 x86_64) - and therefore I expected it to work as smoothly as before.
But now I have a problem. After the installation and starting the service, I wanted to check through my browser if everything is OK.
So I just opened http://xxx.xxx.xxx.xxx/ocpu like it worked on my other server. This time my browser doesn't show the OpenCPU API Explorer, but the following message:
Failed to set rlimit. ENOSYS
In call:
rlimit_wrapper("rlimit_as", hardlim, softlim, pid, verbose)
The server only has 1GB of physical memory, so I thought changing the "rlimit.as" to 1e9 instead of the standrd 2e9 would fix the problem (I also tried 750000000 and 500000000), but nothing helped (of course I restarted the service opencpu again after each change).
I also think that this is not the problem, because I guess the server would use virtual memory when an operation uses more than one GB.
I think the problem has to do with RAppArmor. So I tried to disable it and restart opencpu, but the problem didn't vanish:
$ sudo aa-disable usr.bin.r
Disabling /etc/apparmor.d/usr.bin.r.
Traceback (most recent call last):
File "/usr/sbin/aa-disable", line 30, in
tool.cmd_disable()
File "/usr/lib/python3/dist-packages/apparmor/tools.py", line 148, in cmd_disable
raise apparmor.AppArmorException(cmd_info[1])
apparmor.common.AppArmorException: 'Warning: unable to find a suitable fs in /proc/mounts, is it mounted?\nUse --subdomainfs to override.\n'
So does anyone know what the problem here could be or has any suggestions where to look for a solution (I tried to google already, but didn't find anything helpful)?
I don't think anything of the following is the cause of the problem, but since I'm not sure, I add these warnings anyways:
The only strange thing I encountered during the OpenCPU installation was this message (which appeared 4 times):
iptables v1.4.21: can't initialize iptables table `nat': Table does not exist (do you need to insmod?)
Perhaps iptables or your kernel needs to be upgraded.
But afterwards it said:
* Reloading nginx configuration nginx [ OK ]
OK
Setting up opencpu (1.4.4-trusty15) ...
Also when I tried to install RAppArmor separately, I got the following warning:
perl: warning: Please check that your locale settings:
LANGUAGE = (unset),
LC_ALL = (unset),
LC_CTYPE = "UTF-8",
LANG = (unset)
are supported and installed on your system.
perl: warning: Falling back to the standard locale ("C").
locale: Cannot set LC_CTYPE to default locale: No such file or directory
locale: Cannot set LC_ALL to default locale: No such file or directory
Selecting previously unselected package r-cran-rapparmor.
And also this one:
Warning: unable to find a suitable fs in /proc/mounts, is it mounted?\nUse --subdomainfs to override.\n
Thanks in advance!

It looks like your new hosting provider uses some sort of virtualization system that has a shared kernel which limits all kind of linux functionality, including rlimit, iptables and probably apparmor. Is an actual cloud host, or something you setup yourself?
It would be helpful to debug this in R (outside of opencpu). On your server, start R in the console and type:
library(RAppArmor, lib="/usr/lib/opencpu/library")
rlimit_as(1e9)
rlimit_fsize(1e9)
rlimit_cpu(1e5)

Related

github actions 'SSL connect error' on R package check on ubuntu but not macOS or windows

I'm hitting an SSL error in a ubuntu session of GitHub actions that I'm not sure I understand. these are the three lines of R code in the GitHub action that works on windows and macOS but fail on Ubuntu:
tf <- tempfile()
this_url <- "https://webfs.oecd.org/piaac/puf-data/SAS/SAS7BDAT/prgusap1_2012.sas7bdat"
download.file( this_url , tf , mode = 'wb' )
You can see the windows/macOS successes and ubuntu failures at: https://github.com/asdfree/piaac/actions/runs/4130891484
From what I've found elsewhere, it looks like I need to use OpenSSL on the Linux runner of the GitHub Actions.
I found some examples of how to use OpenSSL within an r.yml file here: https://github.com/jeroen/testbug/blob/929151a0f19ed029d0ae34a7b3661d453974de53/.github/workflows/test.yaml
But my attempt to modify the r.yml file didn't seem to solve the issue: https://github.com/asdfree/piaac/commit/9eb93f8ac8c2eae61300364337b6a357ba56d9e7
i've also attempted three alternatives to download.file() -- ubuntu still fails where windows and macOS succeeds. the error here shows up as unsafe legacy renegotiation disabled even when i use ssl.verifypeer=FALSE
https://github.com/asdfree/piaac/commit/07cb4808a4d027f28d6e8cefdf5af09493dcb309
https://github.com/asdfree/piaac/actions/runs/4131647361
https://github.com/asdfree/piaac/commit/468588f6813cfe734d7b11b875070b331189cbc0
https://github.com/asdfree/piaac/actions/runs/4131695976
https://github.com/asdfree/piaac/commit/77e228ef72fc3a781dba51c23ceb9f54f0fac286
https://github.com/asdfree/piaac/actions/runs/4131784227
Any advice about how to work around this issue would be appreciated. Thanks!

Set up rstudio-server on macOS

I want to set up rstudio-server on an iMac with support for multiple users and remote login. I followed the steps in the INSTALL tutorial: I built the source, set up the configuration files and the launchd daemon. At first, it works fine, but after some time, I get these warnings/errors when I plot:
2022-06-09 08:02:29.438 rsession[3050:139329] XType: failed to connect - Error Domain=NSCocoaErrorDomain Code=4099 "The connection to service named com.apple.fonts was invalidated: failed at lookup with error 3 - No such process." UserInfo={NSDebugDescription=The connection to service named com.apple.fonts was invalidated: failed at lookup with error 3 - No such process.}
2022-06-09 08:02:29.438 rsession[3050:139329] Font server protocol version mismatch (expected:5 got:0), falling back to local fonts
2022-06-09 08:02:29.438 rsession[3050:139329] XType: unable to make a connection to the font daemon!
2022-06-09 08:02:29.438 rsession[3050:139329] XType: XTFontStaticRegistry is enabled as fontd is not available.
Then I can't plot any more unless I restart R and re-run my code. Do you know what could be the issue? I could not get any help when opening an issue on the rstudio-server github since MacOS is not officially supported.
I was also looking at running rstudio-server via docker, but I couldn't find a good way to map the user namespace from macOS to the container.
Any help or suggestion would be greatly appreciated!
EDIT: It seems I was able to solve the issue by launching the fontd daemon with:
sudo launchctl load -w /System/Library/LaunchAgents/com.apple.fontd.useragent.plist
This seems like an issue with the MacOS font daemon, not with RStudio itself.
Someone reported a similar issue on PhantomJS. Rebooting resolved it for them.
This answer reported the same error for a different build, and they were able to resolve it by installing the correct "Apple Worldwide Developer Relations Certification Authority" in Keychain:
The one I had had an expiration date of February 2023. I deleted that one and went here, downloaded the one called "Worldwide Developer Relations - G3 (Expiring 02/20/2030 00:00:00 UTC)", then retried the build and it worked.

Hostapd start error

make wthis this manual
http://wireless.kernel.org/en/users/Documentation/hostapd
with this config file
interface=wlan2
bridge=br0
driver=nl80211
ssid=SupaAP
country_code=RU
hw_mode=g
channel=5
preamble=1
macaddr_acl=0
auth_algs=1
logger_syslog=-1
logger_syslog_level=3
logger_stdout=-1
logger_stdout_level=2
ignore_broadcast_ssid=0
ieee80211n=1
ht_capab=[SHORT-GI-20][RX-STBC1]
wmm_enabled=1
and i have error
oot#Cubian:/home/cubie/wif/hostapd-2.1/hostapd# ./hostapd /etc/hostapd/hostapd.conf
Configuration file: /etc/hostapd/hostapd.conf
Line 16: unknown configuration item 'ieee80211n'
Line 17: unknown configuration item 'ht_capab'
2 errors found in configuration file '/etc/hostapd/hostapd.conf'
Failed to set up interface with /etc/hostapd/hostapd.conf
Failed to initialize interfac
in old version i dont have thsi error
It appears that the problem is that hostapd 2.1 is now treating an error it had differently.
This is reproducible on Ubuntu desktop versions, as the resource (WLAN) is busy.
If one turns off the programs that are accessing the resource, hostapd has a chance to grab it and work.
In Ubuntu desktop 14.04 beta, a solution is to turn off the programs that are using the wlan in question.
This worked for me:
sudo nmcli nm wifi off
sudo rfkill unblock wlan
then hostapd can start normally from command line. Of course, if you want hostapd to start on boot you must insure that the network manager is not grabbing the resource ahead of time.
SOLVED
in compile conf i uncomment string
CONFIG_IEEE80211N=y
I have found this link explaining the cause of the error and how to solve it.
https://bugs.archlinux.org/task/20269
Also I have found this other link http://blog.mirjamali.com/en/IT/Linux/hostapd which I followed and it is working with me check the configuration part.
My OS is ubuntu 12.4
start your hostapd with
hostapd -dd /etc/hostapd/hostapd.conf
you will get more information for diagnostics. In which old version you did not get the error? Did you update hostapd? Or changed your wifi adapter? which distri you are using?
http://hostap.epitest.fi/cgit/hostap/plain/hostapd/hostapd.conf
there is written how the ieee80211n settings are. for me i cant see an error.
if you remove the both lines, the ap is starting correctly?

pgpool-II connection pooling - ERROR: "MD5" authentication with pgpool failed

Using the following for just connection pooling no master_slave or replication: rhel 6, postgresql 9.1.9, & pgpool-II 3.1.3 (also tried 3.2.5)
Followed solution suggested in http://www.pgpool.net/pipermail/pgpool-general/2013-May/001773.html
After following the instructions for MD5 I also tried setting both pg_hba.conf and pool_hba.conf to trust for local and subnet, but still get the following error when attempting to connect to the pool locally:
ERROR: "MD5" authentication with pgpool failed for user foo
Tried locally on Fedora 18 with pg9.2 and pgpool from Fedora repo and worked right out of the box.
At the end of all routes suggested everywhere I could find.
Help would be greatly appreciated.
After having hit the same problem the solution was to change ownership of the pool_passwd file to postgres.
Even though this file has a 644 permission, if owner isn't postgres you'll always get the aforementioned error. I guess this file's owner and the user running pgpool must match.
I'm running PosgreSQL 9.2 and pgpool-II 3.3.2, BTW.

ORA-12547: TNS Lost Contact when running DBCA on Oracle 11g installation on Ubuntu Linux 12.04 64 bit

I'm trying to create a database using DBCA on Oracle 11g installation on Ubuntu Linux 12.04 64 bit.
I followed the instructions here, but I get
ORA-12547: TNS Lost Contact when running DBCA.
Below are the details. Can someone assist with the solution?
Instead of using /opt/oracle as the "oracle" user home, I used /home/oracle
I did not install the libstdc++5 in 32 bit version
I did everything else the same as the posting
Installation resulted in "missing packages". I tried to do an apt-get install for these packages from ubuntu, but ubuntu says that they don't exist.
Then I saw in the instructions:
Once you will reach the "pre-reqs" screen, check "Ignore all" to continue the installation.
When running ./dbca from $ORACLE_HOME/bin, it fails with ORA-12547.
I checked $ORACLE_HOME/network/admin and listener.ora , sqlnet.ora , and tnsnames.ora all look OK.
However, I think that tnsnames.ora is not being read properly, because ./tnsping fails and the error message states that "EZ Connect" was used.
But in my sqlnet.ora , I have
names.directory_lookup = (TNSNAMES,EZCONNECT)
It should use EZ Connect only after tnsnames is tried.
Also, I sometimes get ORA-12541: No listener. I tried running ./netca. Everything is OK until I perform a test on the listener, and it fails.
I can't run ./lsnrctl. Absolutely nothing happens for this, as well as lsnrctl start, stop, status.
I can't go through sqlplus. If I run ./sqlplus , it asks me for username/password directly.
If I do ./sqlplus / as sysdba, then this results in "ORA-12547: TNS lost contact".
All environment variables are set correctly in .bashrc.
I tried re-running root.sh , but the problem is not fixed.
/etc/oratab is OK
/etc/hosts is OK, but I can't always ping the "localhost" or "127.0.0.1", or "ubuntu" or "127.0.1.1"
The same TNS or Listener errors display.
When I login in oracle (sqlplus system/pass as sysdba), I got this:
ERROR:  
ORA-12547: TNS :lost contact when try to connect to Oracle.
First, I think the server is down, but I check it, it is OK. And so many body say 'chmod 6751 oracle', I did it, but I got another error:
ERROR:
ORA-01031: insufficient privileges
Enter user-name:
finally, I switch the system user from root to oracle. And I login success.
Ensure the DB is up and running and you can connect locally AS SYSDBA to the database
using Oracle binaries owner (usually oracle:oinstall Unix / Linux user). If it does not
work, probably you encounter a different problem.
1. Check privileges of an Oracle file on Unix / Linux host where database is running:
cd $ORACLE_HOME/bin
ls -ltr oracle
2. Change permissions as below:
chmod 6751 oracle
ls -ltr oracle
This code may help you lot.

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