Unexplainably high memory usage in idle

Neth · 04-06-2012, 06:06 AM

Hi,

I'm not sure whether this fits here, but I did not find any other forum this question really belongs to neither. I have seen quite some discussions about this kind of topic but could not figure out any solution for my problem from the information provided in different posts.
My problem is, that my machine seems to be using up memory and wont show me what it is doing with it. Going through the different tools, I don't find any useful hint as to what about 4 gigabyte of my memory are used for.
When starting my machine it takes up about 1 gig of ram, which is okish, given I have about 16 Gig. However after some work (python programming) the system is getting more and more crowded. If I then close everything the system tells me it is now using about 5 gigabyte of memory. My first thoughts were: "Ok, buffers, or some file-cache", but that's not what it is. vmstat, free and top tell me that about 7.5 GB of memory are free and I got a buffer+cache size of about 3 GB. leaving 5 GB of used memory:
"vmstat"

Code:

procs -----------memory---------- ---swap-- -----io---- --system-- -----cpu-----
 r  b   swpd   free   buff  cache   si   so    bi    bo   in   cs us sy id wa st
 0  0      0 7552908 314796 2733176    0    0     4     3   23   48  2  1 97  0  0

Top:

Code:

Mem:  16428684k total,  8965480k used,  7463204k free,   315436k buffers
Swap: 23446860k total,        0k used, 23446860k free,  2739068k cached

free -m :

Code:

             total       used       free     shared    buffers     cached
Mem:         16043       8774       7269          0        308       2674
-/+ buffers/cache:       5791      10252
Swap:        22897          0      22897

Finally some information from cat /proc/meminfo though I must admit that I do not fully understand it and the reason for my high memory usage might well be explained in there:
cat /proc/meminfo:

Code:

MemTotal:       16428684 kB
MemFree:         7454456 kB
Buffers:          315400 kB
Cached:          2739024 kB
Active:          1716572 kB
Inactive:        2056224 kB
Active(anon):     720536 kB
Inactive(anon):    10312 kB
Active(file):     996036 kB
Inactive(file):  2045912 kB
Unevictable:       12548 kB
Mlocked:           12548 kB
SwapTotal:      23446860 kB
SwapFree:       23446860 kB
Dirty:               440 kB
AnonPages:        730924 kB
Mapped:           183684 kB
Shmem:             10564 kB
Slab:             266756 kB
SReclaimable:     234144 kB
SUnreclaim:        32612 kB
KernelStack:        3640 kB
PageTables:        61292 kB
CommitLimit:    31661200 kB
Committed_AS:    2065088 kB
VmallocTotal:   34359738367 kB
VmallocUsed:      348916 kB
VmallocChunk:   34359374396 kB
Hugepagesize:       2048 kB
DirectMap4k:     4597248 kB
DirectMap2M:    12138496 kB

Any Ideas what else I could do to try and figure out, what is using up my memory?

Cheers

syg00 · 04-06-2012, 06:18 AM

Edit that post and change the [quote] tags to [code] so we can read it pls.
What else do you have running - Oracle maybe ?.

Neth · 04-06-2012, 06:30 AM

I have nothing running which I would know of.
It's a Fedora 13 with Gnome 2.30.2

H_TeXMeX_H · 04-06-2012, 09:22 AM

Run 'top' and see what is using the most memory.

johnsfine · 04-06-2012, 09:46 AM

Quote:

Originally Posted by H_TeXMeX_H

Run 'top' and see what is using the most memory.

I assume by "using ... memory" you mean the RES column of top. (If you mean the VIRT column, it is not relevant to the current situation. If you mean the %MEM column, it is a cruder measure of the same info as RES).

Neth, if you type Oq in top (capital O, lower case q) it will bring the processes with highest RES to the top of the display.

I would have expected the memory identified in RES in top would be included in AnonPages or Mapped in meminfo, which we have already seen are small relative to apparently used ram.

So I would be surprised if H_TeXMeX_H's suggestion points to the answer, but I would be curious to see what it yields anyway.

Neth · 04-06-2012, 10:25 AM

The current top output is posted below. The sum of RES values adds up to something about 2GB. same as the ps output before.
I know I am running some things now (python, ff, java, acroreader) which were not running before so thats the difference between the 1.2 GB from the ps above and the 2GB now.
Still 10GB used - 3 GB buffers - 2 GB programs is FAR from 0 and now even higher than the 5GB idle before (rather 6 GB idle mem usage). So I am still missing a lot of memory without having any clue where it might be hiding...

Code:

top - 16:00:55 up 1 day,  1:12,  3 users,  load average: 1.15, 0.66, 0.31
Tasks: 302 total,   2 running, 300 sleeping,   0 stopped,   0 zombie
Cpu(s): 18.9%us,  1.0%sy,  0.0%ni, 80.1%id,  0.0%wa,  0.0%hi,  0.0%si,  0.0%st
Mem:  16428684k total, 10834324k used,  5594360k free,   325984k buffers
Swap: 23446860k total,        0k used, 23446860k free,  2763828k cached

PID	USER	PR	NI	VIRT	RES	SHR	S	%CPU	%MEM	TIME+	COMMAND
21694	myuser	20	0	1072m	430m	24m	R	110.6	2.7	22:52.67	python
20713	myuser	20	0	1318m	223m	29m	S	3.9	1.4	49:42.78	firefox
25652	myuser	20	0	6089m	141m	20m	S	0	0.9	00:07.03	java
21098	myuser	20	0	846m	110m	29m	S	0	0.7	00:44.47	thunderbird-bin
25691	myuser	20	0	179m	104m	26m	S	0	0.7	00:39.93	acroread
20971	myuser	20	0	1005m	95m	59m	S	0	0.6	01:04.73	scalc.bin
2169	root	20	0	204m	59m	20m	S	13.8	0.4	39:43.82	Xorg
20779	myuser	20	0	226m	54m	15m	S	2	0.3	12:35.80	npviewer.bin
2093	myuser	20	0	91052	32m	5176	S	0	0.2	00:23.95	Xvnc
2369	myuser	20	0	474m	27m	10m	S	0	0.2	00:06.88	gnome-settings-
2757	myuser	20	0	274m	25m	4908	S	0	0.2	00:16.07	gnome-screensav
2470	myuser	20	0	345m	22m	9.8m	S	0	0.1	00:00.26	applet.py
2715	myuser	20	0	345m	22m	9.8m	S	0	0.1	00:01.10	applet.py
22036	myuser	20	0	454m	21m	14m	S	11.8	0.1	40:33.61	gnome-system-mo
20957	myuser	20	0	839m	21m	13m	S	0	0.1	00:07.87	gedit
2688	myuser	20	0	461m	20m	13m	S	0	0.1	00:13.52	gnome-panel
3023	myuser	20	0	466m	19m	15m	S	0	0.1	00:02.10	kded4
2487	myuser	20	0	652m	18m	14m	S	0	0.1	00:00.11	gnote
2691	myuser	20	0	918m	18m	14m	S	0	0.1	00:07.54	nautilus
2420	myuser	20	0	917m	17m	13m	S	0	0.1	00:06.17	nautilus
2733	myuser	20	0	641m	17m	13m	S	0	0.1	00:00.09	gnote
1956	mysql	20	0	368m	16m	3020	S	0	0.1	00:19.98	mysqld
2396	myuser	20	0	444m	15m	10m	S	0	0.1	00:05.74	gnome-panel
21667	myuser	20	0	397m	14m	10m	S	2	0.1	00:09.85	gnome-terminal
2495	myuser	20	0	461m	14m	10m	S	0	0.1	00:01.81	clock-applet
2679	myuser	20	0	375m	14m	10m	S	0	0.1	00:41.73	gnome-settings-
2686	myuser	20	0	552m	14m	10m	S	0	0.1	00:55.40	metacity
2728	myuser	20	0	446m	14m	10m	S	0	0.1	02:02.29	wnck-applet
2744	myuser	20	0	466m	14m	11m	S	0	0.1	00:01.85	clock-applet
1493	root	20	0	16648	12m	1920	S	0	0.1	00:03.77	mdmon
2452	myuser	20	0	572m	12m	9.8m	S	0	0.1	00:00.26	gpk-update-icon
3075	myuser	20	0	395m	12m	9076	S	0	0.1	00:03.27	notification-da
2499	myuser	20	0	429m	11m	9428	S	0	0.1	00:00.06	gdm-user-switch
2743	myuser	20	0	429m	11m	9452	S	0	0.1	00:00.09	gdm-user-switch
2395	myuser	20	0	387m	10m	8076	S	0	0.1	00:00.31	metacity
2429	myuser	20	0	295m	10m	9096	S	0	0.1	00:00.08	wnck-applet
2437	myuser	20	0	470m	10m	8264	S	0	0.1	00:00.15	gnome-volume-co
2697	myuser	20	0	470m	10m	8260	S	0	0.1	00:00.15	gnome-volume-co
2707	myuser	20	0	265m	10m	8988	S	0	0.1	00:00.20	gpk-update-icon
8805	myuser	20	0	391m	9900	7884	S	0	0.1	00:00.07	notification-da
2712	myuser	20	0	544m	9464	6968	S	0	0.1	00:00.11	nm-applet
2730	myuser	20	0	427m	9196	6988	S	0	0.1	00:00.05	trashapplet
2022	root	20	0	283m	9000	5416	S	0	0.1	00:01.58	httpd
2431	myuser	20	0	427m	8804	6648	S	0	0.1	00:00.04	trashapplet
2746	myuser	20	0	278m	7768	6212	S	0	0	00:00.11	notification-ar
2498	myuser	20	0	278m	7464	5980	S	0	0	00:00.04	notification-ar
2400	gdm	20	0	237m	7132	5608	S	0	0	00:00.03	polkit-gnome-au
1653	root	20	0	177m	7048	2896	S	0	0	00:02.51	cupsd
2704	myuser	20	0	247m	6880	5516	S	0	0	00:00.84	gnome-power-man
2481	myuser	20	0	255m	6840	5072	S	0	0	00:02.43	gnome-screensav
2445	myuser	20	0	246m	6608	5252	S	0	0	00:00.42	gnome-power-man
2716	myuser	20	0	246m	6456	5092	S	0	0	00:00.22	gdu-notificatio
2471	myuser	20	0	246m	6424	5060	S	0	0	00:00.22	gdu-notificatio
2479	myuser	20	0	223m	6416	5128	S	0	0	00:00.06	bluetooth-apple
2724	myuser	20	0	223m	6416	5128	S	0	0	00:00.04	bluetooth-apple
2698	myuser	20	0	244m	6344	5036	S	0	0	00:00.07	vino-server
2440	myuser	20	0	244m	6332	5036	S	0	0	00:00.08	vino-server
3021	myuser	20	0	271m	6332	5248	S	0	0	00:00.01	klauncher
2583	myuser	20	0	240m	6320	4940	S	0	0	00:00.17	gnome-session
2291	myuser	20	0	240m	6312	4940	S	0	0	00:00.16	gnome-session
2407	myuser	9	-11	446m	6132	3900	S	0	0	05:31.25	pulseaudio
2671	myuser	20	0	130m	5784	2088	S	0	0	00:15.46	gconfd-2
2480	myuser	20	0	222m	5772	4624	S	0	0	00:00.03	abrt-applet
2725	myuser	20	0	221m	5748	4608	S	0	0	00:00.02	abrt-applet
2336	myuser	20	0	130m	5608	2072	S	0	0	00:00.77	gconfd-2
2068	apache	20	0	283m	5436	616	S	0	0	00:00.00	httpd
2069	apache	20	0	283m	5436	616	S	0	0	00:00.00	httpd
2070	apache	20	0	283m	5436	616	S	0	0	00:00.00	httpd
2071	apache	20	0	283m	5436	616	S	0	0	00:00.00	httpd
2073	apache	20	0	283m	5436	616	S	0	0	00:00.00	httpd
2074	apache	20	0	283m	5436	616	S	0	0	00:00.00	httpd
2075	apache	20	0	283m	5436	616	S	0	0	00:00.00	httpd
2076	apache	20	0	283m	5436	616	S	0	0	00:00.00	httpd
2710	myuser	20	0	219m	5252	4220	S	0	0	00:00.00	polkit-gnome-au
2460	myuser	20	0	219m	5200	4172	S	0	0	00:00.00	polkit-gnome-au
1672	haldaemo	20	0	38380	4800	4040	S	0	0	00:00.61	hald
2005	root	20	0	256m	4680	3496	S	0	0	00:00.25	abrtd
15684	root	20	0	77192	4244	3408	S	0	0	00:00.01	packagekitd
2404	root	20	0	45944	4160	2716	S	0	0	00:00.47	polkitd
1518	root	20	0	73504	4040	3272	S	0	0	00:00.20	NetworkManager
3019	myuser	20	0	241m	4036	2652	S	0	0	00:00.01	kdeinit4
2469	myuser	20	0	120m	3700	3068	S	0	0	00:00.01	deja-dup-monito
2714	myuser	20	0	120m	3700	3068	S	0	0	00:00.00	deja-dup-monito
2571	root	20	0	187m	3344	2464	S	0	0	00:00.01	gdm-session-wor
2166	root	20	0	158m	3268	2540	S	0	0	00:00.03	gdm-simple-slav
2435	myuser	20	0	149m	3256	2516	S	0	0	00:00.44	gvfs-gdu-volume
2690	myuser	20	0	149m	3208	2504	S	0	0	00:00.41	gvfs-gdu-volume
2693	myuser	20	0	999m	3100	2136	S	0	0	00:00.02	bonobo-activati
2443	root	20	0	55220	3004	2280	S	0	0	00:06.41	udisks-daemon
2423	myuser	20	0	679m	2984	2128	S	0	0	00:00.02	bonobo-activati
2223	root	20	0	4019m	2956	2012	S	0	0	00:00.19	console-kit-dae
2748	myuser	20	0	144m	2952	2412	S	0	0	00:00.00	gvfsd-trash
2439	myuser	20	0	144m	2948	2412	S	0	0	00:00.02	gvfsd-trash
2303	root	20	0	49404	2604	2088	S	0	0	00:00.06	upowerd
3124	myuser	20	0	227m	2552	2104	S	0	0	00:00.00	gvfsd-cdda
1527	root	20	0	57948	2400	1932	S	0	0	00:00.04	modem-manager
1508	dbus	20	0	22996	2396	836	S	0	0	00:01.70	dbus-daemon
2436	myuser	20	0	91260	2396	1968	S	0	0	00:00.00	gconf-helper
2762	myuser	20	0	134m	2344	1472	S	0	0	00:00.01	gvfsd-metadata
3121	myuser	20	0	225m	2324	1904	S	0	0	00:00.00	gvfsd-cdda
2551	myuser	20	0	140m	2188	1856	S	0	0	00:00.00	gvfsd-burn
2767	myuser	20	0	140m	2188	1856	S	0	0	00:00.00	gvfsd-burn
1987	root	20	0	74016	2132	668	S	0	0	00:01.47	sendmail
2120	root	20	0	130m	2112	1812	S	0	0	00:00.05	gdm-binary
1530	avahi	20	0	28232	2096	1320	S	0	0	00:13.04	avahi-daemon
2681	myuser	20	0	140m	2096	1748	S	0	0	00:00.01	gvfsd
2375	myuser	20	0	140m	2092	1752	S	0	0	00:00.02	gvfsd
2384	myuser	20	0	267m	2092	1524	S	0	0	00:00.00	gvfs-fuse-daemo
1753	root	20	0	595m	2064	1428	S	0	0	00:00.67	automount
1830	ntp	20	0	30396	2056	1492	S	0	0	00:00.13	ntpd
2576	myuser	20	0	63876	2036	1572	S	0	0	00:00.00	gnome-keyring-d
25608	myuser	20	0	105m	1968	1448	S	0	0	00:00.03	bash
2456	myuser	20	0	149m	1952	1572	S	0	0	00:00.00	gvfs-gphoto2-vo
2696	myuser	20	0	149m	1948	1572	S	0	0	00:00.00	gvfs-gphoto2-vo
21669	myuser	20	0	105m	1940	1448	S	0	0	00:00.02	bash
2464	myuser	20	0	226m	1924	1592	S	0	0	00:01.86	gvfs-afc-volume
2700	myuser	20	0	226m	1920	1588	S	0	0	00:01.72	gvfs-afc-volume
2370	myuser	20	0	156m	1832	1404	S	0	0	00:00.00	gnome-keyring-d
1995	smmsp	20	0	59248	1824	612	S	0	0	00:00.00	sendmail
2558	myuser	20	0	133m	1792	1464	S	0	0	00:00.00	gvfsd-metadata
1438	root	20	0	244m	1704	872	S	0	0	00:00.23	rsyslogd
2534	root	16	-4	103m	1692	1268	S	0	0	00:00.00	sedispatch
2593	myuser	20	0	22116	1620	592	S	0	0	00:01.19	dbus-daemon
1738	root	20	0	91224	1452	704	S	0	0	00:00.12	pcscd
1	root	20	0	19288	1432	1144	S	0	0	00:01.15	init
1866	root	20	0	105m	1428	1192	S	0	0	00:00.01	mysqld_safe
2171	myuser	20	0	21860	1428	592	S	0	0	00:00.14	dbus-daemon
2104	myuser	20	0	38324	1356	1048	S	0	0	00:00.00	vncconfig
2140	root	18	-2	11196	1316	412	S	0	0	00:00.00	udevd
626	root	16	-4	11200	1264	356	S	0	0	00:00.03	udevd
20961	myuser	20	0	103m	1244	1068	S	0	0	00:00.00	soffice
2030	root	20	0	114m	1232	648	S	0	0	00:00.34	crond
25298	myuser	20	0	15140	1228	808	R	0	0	00:00.00	top
1822	root	20	0	51792	1204	680	S	0	0	00:00.00	sshd
2381	root	18	-2	11196	1204	300	S	0	0	00:00.00	udevd
1673	root	20	0	20216	1168	956	S	0	0	00:00.00	hald-runner
1552	rpcuser	20	0	23080	1144	856	S	0	0	00:00.00	rpc.statd
2409	rtkit	21	1	164m	1132	964	S	0	0	00:00.65	rtkit-daemon
3025	myuser	20	0	9276	1084	960	S	0	0	00:00.00	gam_server
25651	myuser	20	0	103m	1028	868	S	0	0	00:00.00	sh
21693	myuser	20	0	105m	1012	516	S	0	0	00:00.00	bash
1485	rpc	20	0	18912	952	692	S	0	0	00:00.08	rpcbind
1702	root	20	0	22336	884	740	S	0	0	00:01.10	hald-addon-inpu
1715	root	20	0	22332	884	736	S	0	0	00:06.46	hald-addon-stor
2529	root	12	-8	82028	796	664	S	0	0	00:00.05	audispd
1717	haldaemo	20	0	17836	764	628	S	0	0	00:00.19	hald-addon-acpi
21668	myuser	20	0	8176	660	560	S	0	0	00:00.00	gnome-pty-helpe
2292	myuser	20	0	42928	656	216	S	0	0	00:00.15	ssh-agent
1664	root	20	0	4032	616	504	S	0	0	00:00.00	acpid
2527	root	16	-4	27576	616	428	S	0	0	00:00.02	auditd
2128	root	20	0	4016	532	460	S	0	0	00:00.00	mingetty
2130	root	20	0	4016	532	460	S	0	0	00:00.00	mingetty
2132	root	20	0	4016	532	460	S	0	0	00:00.00	mingetty
2134	root	20	0	4016	532	460	S	0	0	00:00.00	mingetty
2137	root	20	0	4016	528	460	S	0	0	00:00.00	mingetty
2098	myuser	20	0	12620	516	416	S	0	0	00:00.02	ck-xinit-sessio
2447	root	20	0	44612	500	240	S	0	0	00:03.47	udisks-daemon
2144	myuser	20	0	19980	480	280	S	0	0	00:00.00	dbus-launch
2317	gdm	20	0	19980	472	272	S	0	0	00:00.00	dbus-launch
2592	myuser	20	0	19980	464	268	S	0	0	00:00.00	dbus-launch
1499	root	20	0	6704	424	284	S	0	0	00:00.01	mdadm
1478	root	20	0	9188	420	312	S	0	0	00:06.49	irqbalance
1643	root	20	0	27324	416	208	S	0	0	00:00.00	rpc.idmapd
1554	root	20	0	39052	412	188	S	0	0	00:00.00	wpa_supplicant
2112	root	20	0	21380	372	216	S	0	0	00:00.00	atd
2014	root	20	0	6696	308	212	S	0	0	00:01.69	gpm
1108	root	20	0	6936	228	168	S	0	0	00:00.00	system-setup-ke
1531	avahi	20	0	27612	212	28	S	0	0	00:00.00	avahi-daemon
2	root	20	0	0	0	0	S	0	0	00:00.01	kthreadd
3	root	RT	0	0	0	0	S	0	0	00:00.12	migration/0
4	root	20	0	0	0	0	S	0	0	00:00.77	ksoftirqd/0
5	root	RT	0	0	0	0	S	0	0	00:00.00	watchdog/0
6	root	RT	0	0	0	0	S	0	0	00:00.06	migration/1
7	root	20	0	0	0	0	S	0	0	00:00.69	ksoftirqd/1
8	root	RT	0	0	0	0	S	0	0	00:00.00	watchdog/1
9	root	RT	0	0	0	0	S	0	0	00:00.02	migration/2
10	root	20	0	0	0	0	S	0	0	00:00.35	ksoftirqd/2
11	root	RT	0	0	0	0	S	0	0	00:00.00	watchdog/2
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H_TeXMeX_H · 04-06-2012, 10:43 AM

Try running 'top' while it is idle.

I'm not sure why python is using so much RAM and CPU usage. Probably you know.

johnsfine · 04-06-2012, 11:00 AM

One wild guess is that there is some "lazy deallocation" mechanism hiding memory.
If that were correct and you ran some operation that uses a lot of physical memory, then once free memory gets low, you would expect the hidden memory to get used in preference to taking away cache.
One possible choice for something that uses a lot of physical ram safely but probably effectively for this purpose would be to copy many GB of data from disk to the null device. I haven't tried it, but I think that should grow the cache consuming almost all free memory and hopefully consuming any hidden forms of free memory.

Neth · 04-06-2012, 11:09 AM

Top would not show any difference apart from the things mentioned above (python,java,acroread,ff, t-bird beeing off). and the according memory not used.
Python was running something at the time I did this top, so it's mem usage + cpu usage are ok. Still this will not in any way explain the huge amount of missing memory.
I will do a top sometime later, but I can't shutdown some stuff at the moment.

About the "copy stuff to the null device", call me stupid, but how best to do this?

sundialsvcs · 04-09-2012, 09:21 AM

With many gigabytes of memory available, and not much if any demand for it, Linux is under no pressure to "clean up" memory. So, it won't.

pan64 · 04-10-2012, 07:21 AM

yes, actually swap is not used at all.

theKbStockpiler · 04-10-2012, 03:13 PM

I have a Server Distro with Gmome2 with almost every Server Application available and my Dual Core is almost at 100 percent at all times but with Xfce it is almost nothing and the CPU usage does not indicate a resource hog in a System Monitor.